0.014119
0.000000
0.000000
0.000000
0.012301
0.000000
0.000000
0.000000
0.006552
0.00000
0.00000
0.00000
Holden, H.M.
Thoden, J.B.
Branch, M.C.
Zimmer, A.L.
Bruender, N.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
70.828
81.297
152.628
C17 H29 N3 O14 P2
561.371
[(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate
dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose (hydrated at C4)
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C17 H21 N4 O9 P
456.344
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
non-polymer
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
P
N
6
N
O
N
7
N
O
N
8
R
C
N
9
N
C
N
10
S
C
N
11
N
C
N
12
N
N
N
13
N
C
N
14
N
O
N
15
N
O
N
16
R
C
N
17
N
C
N
18
N
O
N
19
N
O
N
20
N
O
N
21
N
C
N
22
R
C
N
23
S
C
N
24
N
O
N
25
N
C
N
26
R
C
N
27
N
O
N
28
N
N
N
29
N
C
N
30
N
O
N
31
N
N
N
32
N
C
N
33
N
O
N
34
N
C
N
35
N
C
N
36
N
C
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
N
N
67
S
C
N
68
N
C
N
69
N
O
N
70
N
C
N
71
N
O
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
N
N
80
S
C
N
81
N
C
N
82
N
O
N
83
N
C
N
84
N
C
N
85
N
C
N
86
N
N
N
87
N
C
N
88
N
N
N
89
N
N
N
90
N
O
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
N
N
107
S
C
N
108
N
C
N
109
N
O
N
110
N
C
N
111
N
C
N
112
N
O
N
113
N
N
N
114
N
O
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
N
129
N
O
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
N
N
140
R
C
N
141
N
C
N
142
N
O
N
143
N
C
N
144
N
S
N
145
N
O
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
N
N
154
N
C
N
155
N
O
N
156
N
N
N
157
N
C
N
158
N
O
N
159
N
C
N
160
N
N
Y
161
N
C
Y
162
N
C
Y
163
N
C
N
164
N
C
Y
165
N
C
N
166
N
C
Y
167
N
C
Y
168
N
C
N
169
N
N
N
170
N
C
N
171
N
C
N
172
S
C
N
173
N
O
N
174
S
C
N
175
N
O
N
176
R
C
N
177
N
O
N
178
N
C
N
179
N
O
N
180
N
P
N
181
N
O
N
182
N
O
N
183
N
O
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
O
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
N
N
226
S
C
N
227
N
C
N
228
N
O
N
229
N
C
N
230
N
C
N
231
N
C
N
232
N
O
N
233
N
O
N
234
N
O
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
N
N
245
N
C
N
246
N
C
N
247
N
O
N
248
N
O
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
N
N
255
S
C
N
256
N
C
N
257
N
O
N
258
N
C
Y
259
N
C
Y
260
N
N
Y
261
N
C
Y
262
N
C
Y
263
N
N
N
264
N
O
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
O
N
276
N
H
N
277
N
H
N
278
N
N
N
279
S
C
N
280
N
C
N
281
N
O
N
282
S
C
N
283
N
C
N
284
N
C
N
285
N
C
N
286
N
O
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
N
N
301
S
C
N
302
N
C
N
303
N
O
N
304
N
C
N
305
N
C
N
306
N
C
N
307
N
C
N
308
N
O
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
N
N
323
S
C
N
324
N
C
N
325
N
O
N
326
N
C
N
327
N
C
N
328
N
C
N
329
N
C
N
330
N
N
N
331
N
O
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
N
N
348
S
C
N
349
N
C
N
350
N
O
N
351
N
C
N
352
N
C
N
353
N
S
N
354
N
C
N
355
N
O
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
N
N
368
S
C
N
369
N
C
N
370
N
O
N
371
N
C
Y
372
N
C
Y
373
N
C
Y
374
N
C
Y
375
N
C
Y
376
N
C
Y
377
N
C
N
378
N
O
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
N
N
391
S
C
N
392
N
C
N
393
N
O
N
394
N
C
N
395
N
C
N
396
N
C
N
397
N
O
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
N
N
408
S
C
N
409
N
C
N
410
N
O
N
411
N
C
N
412
N
O
N
413
N
O
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
N
N
422
S
C
N
423
N
C
N
424
N
O
N
425
R
C
N
426
N
O
N
427
N
C
N
428
N
O
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
N
N
439
S
C
N
440
N
C
N
441
N
O
N
442
N
C
Y
443
N
C
Y
444
N
C
Y
445
N
C
Y
446
N
N
Y
447
N
C
Y
448
N
C
Y
449
N
C
Y
450
N
C
Y
451
N
C
N
452
N
O
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
H
N
465
N
N
N
466
S
C
N
467
N
C
N
468
N
O
N
469
N
C
Y
470
N
C
Y
471
N
C
Y
472
N
C
Y
473
N
C
Y
474
N
C
Y
475
N
C
N
476
N
O
N
477
N
O
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
N
N
490
S
C
N
491
N
C
N
492
N
O
N
493
N
C
N
494
N
C
N
495
N
C
N
496
N
O
N
497
N
H
N
498
N
H
N
499
N
H
N
500
N
H
N
501
N
H
N
502
N
H
N
503
N
H
N
504
N
H
N
505
N
H
N
506
N
H
N
507
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
doub
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
doub
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
doub
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
doub
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
doub
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
doub
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
doub
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
doub
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
doub
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
doub
N
152
N
doub
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
doub
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
Y
161
N
doub
Y
162
N
sing
Y
163
N
sing
N
164
N
sing
N
165
N
sing
Y
166
N
doub
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
Y
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
Y
175
N
doub
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
doub
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
doub
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
doub
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
doub
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
doub
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
doub
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
doub
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
Y
261
N
sing
Y
262
N
doub
Y
263
N
doub
N
264
N
sing
Y
265
N
sing
N
266
N
sing
Y
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
doub
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
doub
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
doub
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
doub
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
Y
369
N
doub
Y
370
N
sing
Y
371
N
sing
N
372
N
sing
Y
373
N
doub
N
374
N
sing
Y
375
N
doub
N
376
N
sing
Y
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
doub
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
doub
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
doub
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
doub
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
Y
438
N
doub
Y
439
N
sing
Y
440
N
sing
N
441
N
sing
Y
442
N
doub
Y
443
N
sing
Y
444
N
sing
N
445
N
sing
Y
446
N
sing
Y
447
N
doub
N
448
N
sing
Y
449
N
doub
N
450
N
sing
Y
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
doub
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
Y
466
N
doub
Y
467
N
sing
Y
468
N
sing
N
469
N
sing
Y
470
N
doub
N
471
N
sing
Y
472
N
doub
N
473
N
sing
Y
474
N
sing
N
475
N
sing
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
doub
N
486
N
sing
N
487
N
sing
N
488
N
sing
N
489
N
sing
N
490
N
sing
N
491
N
sing
N
492
N
sing
N
493
N
sing
N
494
N
sing
N
495
N
sing
N
496
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
52
3191
3193
10.1021/bi400407x
23621882
Active site architecture of a sugar N-oxygenase.
2013
10.2210/pdb4kcf/pdb
pdb_00004kcf
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2012-12-09
ADSC QUANTUM 210r
double crystal monochromator Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.979
1.0
19-BM
APS
0.979
SYNCHROTRON
APS BEAMLINE 19-BM
48327.414
FAD-dependent oxidoreductase
1
man
polymer
561.371
[(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate
1
syn
non-polymer
456.344
FLAVIN MONONUCLEOTIDE
1
syn
non-polymer
18.015
water
102
nat
water
no
no
HHHHHHSSGENLYEQGHMPPWTARQDSTTGLYAPVTPAGRVLLDRLAAHLPRIRSTAAEHDRDGTFPTDTFDALRKDGLM
GATVPAELGGLGVDRLYDVAVALLAVARADASTALALHMQLSRGLTLGYEWRHGDERARTLAERILRGMVAGDAVVCSGI
KDHHTAVTTLRPDGAGGWLLSGRKTLVSMAPVGTHFVINARTDGTDGPPRLASPVVTRDTPGFTVLDNWDGLGMRASGTV
DIVFDDCPIPADHVLMRDPVGARNDAVLAGQTVSSVSVLGVYVGVAQAAYDTAVAALERRPEPPQAAALTLVAEIDSRLY
ALRATAGSALTAADALSADLSGDMDERGRQMMRHFQCAKLAVNRLAPEIVSDCLSLVGGASYTAGHPLARLLRDVQAGRF
MQPYAYVDAVDFLSAQALGIERDNNYMSTWAKRSGGNGKSADAAGPRRPTPTSR
HHHHHHSSGENLYEQGHMPPWTARQDSTTGLYAPVTPAGRVLLDRLAAHLPRIRSTAAEHDRDGTFPTDTFDALRKDGLM
GATVPAELGGLGVDRLYDVAVALLAVARADASTALALHMQLSRGLTLGYEWRHGDERARTLAERILRGMVAGDAVVCSGI
KDHHTAVTTLRPDGAGGWLLSGRKTLVSMAPVGTHFVINARTDGTDGPPRLASPVVTRDTPGFTVLDNWDGLGMRASGTV
DIVFDDCPIPADHVLMRDPVGARNDAVLAGQTVSSVSVLGVYVGVAQAAYDTAVAALERRPEPPQAAALTLVAEIDSRLY
ALRATAGSALTAADALSADLSGDMDERGRQMMRHFQCAKLAVNRLAPEIVSDCLSLVGGASYTAGHPLARLLRDVQAGRF
MQPYAYVDAVDFLSAQALGIERDNNYMSTWAKRSGGNGKSADAAGPRRPTPTSR
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
KijD3
46161
Actinomadura kijaniata
469008
Escherichia coli
Rosetta2 (DE3)
Plasmid
pET28
1
2.27
45.89
VAPOR DIFFUSION, HANGING DROP
7.0
25% pentaerythritol propoxylate 5/4
100 mM MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
298.0
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Atomic model
Non-polymer description
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-05-22
1
1
2013-05-29
1
2
2013-12-18
1
3
2023-09-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
X-ray Structure of a KijD3 in Complex with dTDP
RCSB
Y
RCSB
2013-04-24
REL
REL
AKM
[(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate
FMN
FLAVIN MONONUCLEOTIDE
HOH
water
3M9V
PDB ENTRY 3M9V
PDB
experimental model
AKM
1
2
AKM
AKM
501
A
FMN
1
3
FMN
FMN
502
A
HOH
1
4
HOH
HOH
601
A
HOH
2
4
HOH
HOH
602
A
HOH
3
4
HOH
HOH
603
A
HOH
4
4
HOH
HOH
604
A
HOH
5
4
HOH
HOH
605
A
HOH
6
4
HOH
HOH
606
A
HOH
7
4
HOH
HOH
607
A
HOH
8
4
HOH
HOH
608
A
HOH
9
4
HOH
HOH
609
A
HOH
10
4
HOH
HOH
610
A
HOH
11
4
HOH
HOH
611
A
HOH
12
4
HOH
HOH
612
A
HOH
13
4
HOH
HOH
613
A
HOH
14
4
HOH
HOH
614
A
HOH
15
4
HOH
HOH
615
A
HOH
16
4
HOH
HOH
616
A
HOH
17
4
HOH
HOH
617
A
HOH
18
4
HOH
HOH
618
A
HOH
19
4
HOH
HOH
619
A
HOH
20
4
HOH
HOH
620
A
HOH
21
4
HOH
HOH
621
A
HOH
22
4
HOH
HOH
622
A
HOH
23
4
HOH
HOH
623
A
HOH
24
4
HOH
HOH
624
A
HOH
26
4
HOH
HOH
625
A
HOH
27
4
HOH
HOH
626
A
HOH
28
4
HOH
HOH
627
A
HOH
29
4
HOH
HOH
628
A
HOH
30
4
HOH
HOH
629
A
HOH
31
4
HOH
HOH
630
A
HOH
32
4
HOH
HOH
631
A
HOH
33
4
HOH
HOH
632
A
HOH
34
4
HOH
HOH
633
A
HOH
35
4
HOH
HOH
634
A
HOH
36
4
HOH
HOH
635
A
HOH
37
4
HOH
HOH
636
A
HOH
38
4
HOH
HOH
637
A
HOH
39
4
HOH
HOH
638
A
HOH
40
4
HOH
HOH
639
A
HOH
41
4
HOH
HOH
640
A
HOH
42
4
HOH
HOH
641
A
HOH
43
4
HOH
HOH
642
A
HOH
44
4
HOH
HOH
643
A
HOH
45
4
HOH
HOH
644
A
HOH
47
4
HOH
HOH
645
A
HOH
48
4
HOH
HOH
646
A
HOH
49
4
HOH
HOH
647
A
HOH
50
4
HOH
HOH
648
A
HOH
51
4
HOH
HOH
649
A
HOH
53
4
HOH
HOH
650
A
HOH
54
4
HOH
HOH
651
A
HOH
55
4
HOH
HOH
652
A
HOH
56
4
HOH
HOH
653
A
HOH
57
4
HOH
HOH
654
A
HOH
58
4
HOH
HOH
655
A
HOH
59
4
HOH
HOH
656
A
HOH
60
4
HOH
HOH
657
A
HOH
61
4
HOH
HOH
658
A
HOH
62
4
HOH
HOH
659
A
HOH
63
4
HOH
HOH
660
A
HOH
64
4
HOH
HOH
661
A
HOH
65
4
HOH
HOH
662
A
HOH
66
4
HOH
HOH
663
A
HOH
67
4
HOH
HOH
664
A
HOH
68
4
HOH
HOH
665
A
HOH
69
4
HOH
HOH
666
A
HOH
70
4
HOH
HOH
667
A
HOH
71
4
HOH
HOH
668
A
HOH
73
4
HOH
HOH
669
A
HOH
74
4
HOH
HOH
670
A
HOH
75
4
HOH
HOH
671
A
HOH
76
4
HOH
HOH
672
A
HOH
77
4
HOH
HOH
673
A
HOH
78
4
HOH
HOH
674
A
HOH
79
4
HOH
HOH
675
A
HOH
80
4
HOH
HOH
676
A
HOH
81
4
HOH
HOH
677
A
HOH
82
4
HOH
HOH
678
A
HOH
83
4
HOH
HOH
679
A
HOH
84
4
HOH
HOH
680
A
HOH
85
4
HOH
HOH
681
A
HOH
86
4
HOH
HOH
682
A
HOH
87
4
HOH
HOH
683
A
HOH
88
4
HOH
HOH
684
A
HOH
89
4
HOH
HOH
685
A
HOH
90
4
HOH
HOH
686
A
HOH
91
4
HOH
HOH
687
A
HOH
93
4
HOH
HOH
688
A
HOH
94
4
HOH
HOH
689
A
HOH
95
4
HOH
HOH
690
A
HOH
97
4
HOH
HOH
691
A
HOH
98
4
HOH
HOH
692
A
HOH
99
4
HOH
HOH
693
A
HOH
100
4
HOH
HOH
694
A
HOH
102
4
HOH
HOH
695
A
HOH
103
4
HOH
HOH
696
A
HOH
104
4
HOH
HOH
697
A
HOH
105
4
HOH
HOH
698
A
HOH
106
4
HOH
HOH
699
A
HOH
108
4
HOH
HOH
700
A
HOH
109
4
HOH
HOH
701
A
HOH
110
4
HOH
HOH
702
A
n
1
-16
A
n
2
-15
A
n
3
-14
A
n
4
-13
A
n
5
-12
A
n
6
-11
A
n
7
-10
A
n
8
-9
A
n
9
-8
A
n
10
-7
A
n
11
-6
A
n
12
-5
A
n
13
-4
A
n
14
-3
A
n
15
-2
A
n
16
-1
A
n
17
0
A
n
18
1
A
n
19
2
A
n
20
3
A
n
21
4
A
n
22
5
A
n
23
6
A
n
24
7
A
n
25
8
A
ASP
9
n
26
ASP
9
A
SER
10
n
27
SER
10
A
THR
11
n
28
THR
11
A
THR
12
n
29
THR
12
A
GLY
13
n
30
GLY
13
A
LEU
14
n
31
LEU
14
A
TYR
15
n
32
TYR
15
A
ALA
16
n
33
ALA
16
A
PRO
17
n
34
PRO
17
A
VAL
18
n
35
VAL
18
A
THR
19
n
36
THR
19
A
PRO
20
n
37
PRO
20
A
ALA
21
n
38
ALA
21
A
GLY
22
n
39
GLY
22
A
ARG
23
n
40
ARG
23
A
VAL
24
n
41
VAL
24
A
LEU
25
n
42
LEU
25
A
LEU
26
n
43
LEU
26
A
ASP
27
n
44
ASP
27
A
ARG
28
n
45
ARG
28
A
LEU
29
n
46
LEU
29
A
ALA
30
n
47
ALA
30
A
ALA
31
n
48
ALA
31
A
HIS
32
n
49
HIS
32
A
LEU
33
n
50
LEU
33
A
PRO
34
n
51
PRO
34
A
ARG
35
n
52
ARG
35
A
ILE
36
n
53
ILE
36
A
ARG
37
n
54
ARG
37
A
SER
38
n
55
SER
38
A
THR
39
n
56
THR
39
A
ALA
40
n
57
ALA
40
A
ALA
41
n
58
ALA
41
A
GLU
42
n
59
GLU
42
A
HIS
43
n
60
HIS
43
A
ASP
44
n
61
ASP
44
A
ARG
45
n
62
ARG
45
A
ASP
46
n
63
ASP
46
A
GLY
47
n
64
GLY
47
A
THR
48
n
65
THR
48
A
PHE
49
n
66
PHE
49
A
PRO
50
n
67
PRO
50
A
THR
51
n
68
THR
51
A
ASP
52
n
69
ASP
52
A
THR
53
n
70
THR
53
A
PHE
54
n
71
PHE
54
A
ASP
55
n
72
ASP
55
A
ALA
56
n
73
ALA
56
A
LEU
57
n
74
LEU
57
A
ARG
58
n
75
ARG
58
A
LYS
59
n
76
LYS
59
A
ASP
60
n
77
ASP
60
A
GLY
61
n
78
GLY
61
A
LEU
62
n
79
LEU
62
A
MET
63
n
80
MET
63
A
GLY
64
n
81
GLY
64
A
ALA
65
n
82
ALA
65
A
THR
66
n
83
THR
66
A
VAL
67
n
84
VAL
67
A
PRO
68
n
85
PRO
68
A
ALA
69
n
86
ALA
69
A
GLU
70
n
87
GLU
70
A
LEU
71
n
88
LEU
71
A
GLY
72
n
89
GLY
72
A
GLY
73
n
90
GLY
73
A
LEU
74
n
91
LEU
74
A
GLY
75
n
92
GLY
75
A
VAL
76
n
93
VAL
76
A
ASP
77
n
94
ASP
77
A
ARG
78
n
95
ARG
78
A
LEU
79
n
96
LEU
79
A
TYR
80
n
97
TYR
80
A
ASP
81
n
98
ASP
81
A
VAL
82
n
99
VAL
82
A
ALA
83
n
100
ALA
83
A
VAL
84
n
101
VAL
84
A
ALA
85
n
102
ALA
85
A
LEU
86
n
103
LEU
86
A
LEU
87
n
104
LEU
87
A
ALA
88
n
105
ALA
88
A
VAL
89
n
106
VAL
89
A
ALA
90
n
107
ALA
90
A
ARG
91
n
108
ARG
91
A
ALA
92
n
109
ALA
92
A
ASP
93
n
110
ASP
93
A
ALA
94
n
111
ALA
94
A
SER
95
n
112
SER
95
A
THR
96
n
113
THR
96
A
ALA
97
n
114
ALA
97
A
LEU
98
n
115
LEU
98
A
ALA
99
n
116
ALA
99
A
LEU
100
n
117
LEU
100
A
HIS
101
n
118
HIS
101
A
MET
102
n
119
MET
102
A
GLN
103
n
120
GLN
103
A
LEU
104
n
121
LEU
104
A
SER
105
n
122
SER
105
A
ARG
106
n
123
ARG
106
A
GLY
107
n
124
GLY
107
A
LEU
108
n
125
LEU
108
A
THR
109
n
126
THR
109
A
LEU
110
n
127
LEU
110
A
GLY
111
n
128
GLY
111
A
TYR
112
n
129
TYR
112
A
GLU
113
n
130
GLU
113
A
TRP
114
n
131
TRP
114
A
ARG
115
n
132
ARG
115
A
HIS
116
n
133
HIS
116
A
GLY
117
n
134
GLY
117
A
ASP
118
n
135
ASP
118
A
GLU
119
n
136
GLU
119
A
ARG
120
n
137
ARG
120
A
ALA
121
n
138
ALA
121
A
ARG
122
n
139
ARG
122
A
THR
123
n
140
THR
123
A
LEU
124
n
141
LEU
124
A
ALA
125
n
142
ALA
125
A
GLU
126
n
143
GLU
126
A
ARG
127
n
144
ARG
127
A
ILE
128
n
145
ILE
128
A
LEU
129
n
146
LEU
129
A
ARG
130
n
147
ARG
130
A
GLY
131
n
148
GLY
131
A
MET
132
n
149
MET
132
A
VAL
133
n
150
VAL
133
A
ALA
134
n
151
ALA
134
A
GLY
135
n
152
GLY
135
A
ASP
136
n
153
ASP
136
A
ALA
137
n
154
ALA
137
A
VAL
138
n
155
VAL
138
A
VAL
139
n
156
VAL
139
A
CYS
140
n
157
CYS
140
A
SER
141
n
158
SER
141
A
GLY
142
n
159
GLY
142
A
ILE
143
n
160
ILE
143
A
LYS
144
n
161
LYS
144
A
ASP
145
n
162
ASP
145
A
HIS
146
n
163
HIS
146
A
HIS
147
n
164
HIS
147
A
THR
148
n
165
THR
148
A
ALA
149
n
166
ALA
149
A
VAL
150
n
167
VAL
150
A
THR
151
n
168
THR
151
A
THR
152
n
169
THR
152
A
LEU
153
n
170
LEU
153
A
ARG
154
n
171
ARG
154
A
PRO
155
n
172
PRO
155
A
ASP
156
n
173
ASP
156
A
GLY
157
n
174
GLY
157
A
ALA
158
n
175
ALA
158
A
GLY
159
n
176
GLY
159
A
GLY
160
n
177
GLY
160
A
TRP
161
n
178
TRP
161
A
LEU
162
n
179
LEU
162
A
LEU
163
n
180
LEU
163
A
SER
164
n
181
SER
164
A
GLY
165
n
182
GLY
165
A
ARG
166
n
183
ARG
166
A
LYS
167
n
184
LYS
167
A
THR
168
n
185
THR
168
A
LEU
169
n
186
LEU
169
A
VAL
170
n
187
VAL
170
A
SER
171
n
188
SER
171
A
MET
172
n
189
MET
172
A
ALA
173
n
190
ALA
173
A
PRO
174
n
191
PRO
174
A
VAL
175
n
192
VAL
175
A
GLY
176
n
193
GLY
176
A
THR
177
n
194
THR
177
A
HIS
178
n
195
HIS
178
A
PHE
179
n
196
PHE
179
A
VAL
180
n
197
VAL
180
A
ILE
181
n
198
ILE
181
A
ASN
182
n
199
ASN
182
A
ALA
183
n
200
ALA
183
A
ARG
184
n
201
ARG
184
A
THR
185
n
202
THR
185
A
ASP
186
n
203
ASP
186
A
GLY
187
n
204
GLY
187
A
THR
188
n
205
THR
188
A
ASP
189
n
206
ASP
189
A
GLY
190
n
207
GLY
190
A
PRO
191
n
208
PRO
191
A
PRO
192
n
209
PRO
192
A
ARG
193
n
210
ARG
193
A
LEU
194
n
211
LEU
194
A
ALA
195
n
212
ALA
195
A
SER
196
n
213
SER
196
A
PRO
197
n
214
PRO
197
A
VAL
198
n
215
VAL
198
A
VAL
199
n
216
VAL
199
A
THR
200
n
217
THR
200
A
ARG
201
n
218
ARG
201
A
ASP
202
n
219
ASP
202
A
THR
203
n
220
THR
203
A
PRO
204
n
221
PRO
204
A
GLY
205
n
222
GLY
205
A
PHE
206
n
223
PHE
206
A
THR
207
n
224
THR
207
A
VAL
208
n
225
VAL
208
A
LEU
209
n
226
LEU
209
A
ASP
210
n
227
ASP
210
A
ASN
211
n
228
ASN
211
A
TRP
212
n
229
TRP
212
A
ASP
213
n
230
ASP
213
A
GLY
214
n
231
GLY
214
A
LEU
215
n
232
LEU
215
A
GLY
216
n
233
GLY
216
A
MET
217
n
234
MET
217
A
ARG
218
n
235
ARG
218
A
ALA
219
n
236
ALA
219
A
SER
220
n
237
SER
220
A
GLY
221
n
238
GLY
221
A
THR
222
n
239
THR
222
A
VAL
223
n
240
VAL
223
A
ASP
224
n
241
ASP
224
A
ILE
225
n
242
ILE
225
A
VAL
226
n
243
VAL
226
A
PHE
227
n
244
PHE
227
A
ASP
228
n
245
ASP
228
A
ASP
229
n
246
ASP
229
A
CYS
230
n
247
CYS
230
A
PRO
231
n
248
PRO
231
A
ILE
232
n
249
ILE
232
A
PRO
233
n
250
PRO
233
A
ALA
234
n
251
ALA
234
A
ASP
235
n
252
ASP
235
A
HIS
236
n
253
HIS
236
A
VAL
237
n
254
VAL
237
A
LEU
238
n
255
LEU
238
A
MET
239
n
256
MET
239
A
ARG
240
n
257
ARG
240
A
ASP
241
n
258
ASP
241
A
PRO
242
n
259
PRO
242
A
VAL
243
n
260
VAL
243
A
GLY
244
n
261
GLY
244
A
ALA
245
n
262
ALA
245
A
ARG
246
n
263
ARG
246
A
ASN
247
n
264
ASN
247
A
ASP
248
n
265
ASP
248
A
ALA
249
n
266
ALA
249
A
VAL
250
n
267
VAL
250
A
LEU
251
n
268
LEU
251
A
ALA
252
n
269
ALA
252
A
GLY
253
n
270
GLY
253
A
GLN
254
n
271
GLN
254
A
THR
255
n
272
THR
255
A
VAL
256
n
273
VAL
256
A
SER
257
n
274
SER
257
A
SER
258
n
275
SER
258
A
VAL
259
n
276
VAL
259
A
SER
260
n
277
SER
260
A
VAL
261
n
278
VAL
261
A
LEU
262
n
279
LEU
262
A
GLY
263
n
280
GLY
263
A
VAL
264
n
281
VAL
264
A
TYR
265
n
282
TYR
265
A
VAL
266
n
283
VAL
266
A
GLY
267
n
284
GLY
267
A
VAL
268
n
285
VAL
268
A
ALA
269
n
286
ALA
269
A
GLN
270
n
287
GLN
270
A
ALA
271
n
288
ALA
271
A
ALA
272
n
289
ALA
272
A
TYR
273
n
290
TYR
273
A
ASP
274
n
291
ASP
274
A
THR
275
n
292
THR
275
A
ALA
276
n
293
ALA
276
A
VAL
277
n
294
VAL
277
A
ALA
278
n
295
ALA
278
A
ALA
279
n
296
ALA
279
A
LEU
280
n
297
LEU
280
A
GLU
281
n
298
GLU
281
A
ARG
282
n
299
ARG
282
A
ARG
283
n
300
ARG
283
A
PRO
284
n
301
PRO
284
A
GLU
285
n
302
GLU
285
A
PRO
286
n
303
PRO
286
A
PRO
287
n
304
PRO
287
A
GLN
288
n
305
GLN
288
A
ALA
289
n
306
ALA
289
A
ALA
290
n
307
ALA
290
A
ALA
291
n
308
ALA
291
A
LEU
292
n
309
LEU
292
A
THR
293
n
310
THR
293
A
LEU
294
n
311
LEU
294
A
VAL
295
n
312
VAL
295
A
ALA
296
n
313
ALA
296
A
GLU
297
n
314
GLU
297
A
ILE
298
n
315
ILE
298
A
ASP
299
n
316
ASP
299
A
SER
300
n
317
SER
300
A
ARG
301
n
318
ARG
301
A
LEU
302
n
319
LEU
302
A
TYR
303
n
320
TYR
303
A
ALA
304
n
321
ALA
304
A
LEU
305
n
322
LEU
305
A
ARG
306
n
323
ARG
306
A
ALA
307
n
324
ALA
307
A
THR
308
n
325
THR
308
A
ALA
309
n
326
ALA
309
A
GLY
310
n
327
GLY
310
A
SER
311
n
328
SER
311
A
ALA
312
n
329
ALA
312
A
LEU
313
n
330
LEU
313
A
THR
314
n
331
THR
314
A
ALA
315
n
332
ALA
315
A
ALA
316
n
333
ALA
316
A
ASP
317
n
334
ASP
317
A
ALA
318
n
335
ALA
318
A
LEU
319
n
336
LEU
319
A
SER
320
n
337
SER
320
A
ALA
321
n
338
ALA
321
A
ASP
322
n
339
ASP
322
A
LEU
323
n
340
LEU
323
A
SER
324
n
341
SER
324
A
GLY
325
n
342
GLY
325
A
ASP
326
n
343
ASP
326
A
MET
327
n
344
MET
327
A
ASP
328
n
345
ASP
328
A
GLU
329
n
346
GLU
329
A
ARG
330
n
347
ARG
330
A
GLY
331
n
348
GLY
331
A
ARG
332
n
349
ARG
332
A
GLN
333
n
350
GLN
333
A
MET
334
n
351
MET
334
A
MET
335
n
352
MET
335
A
ARG
336
n
353
ARG
336
A
HIS
337
n
354
HIS
337
A
PHE
338
n
355
PHE
338
A
GLN
339
n
356
GLN
339
A
CYS
340
n
357
CYS
340
A
ALA
341
n
358
ALA
341
A
LYS
342
n
359
LYS
342
A
LEU
343
n
360
LEU
343
A
ALA
344
n
361
ALA
344
A
VAL
345
n
362
VAL
345
A
ASN
346
n
363
ASN
346
A
ARG
347
n
364
ARG
347
A
LEU
348
n
365
LEU
348
A
ALA
349
n
366
ALA
349
A
PRO
350
n
367
PRO
350
A
GLU
351
n
368
GLU
351
A
ILE
352
n
369
ILE
352
A
VAL
353
n
370
VAL
353
A
SER
354
n
371
SER
354
A
ASP
355
n
372
ASP
355
A
CYS
356
n
373
CYS
356
A
LEU
357
n
374
LEU
357
A
SER
358
n
375
SER
358
A
LEU
359
n
376
LEU
359
A
VAL
360
n
377
VAL
360
A
GLY
361
n
378
GLY
361
A
GLY
362
n
379
GLY
362
A
ALA
363
n
380
ALA
363
A
SER
364
n
381
SER
364
A
TYR
365
n
382
TYR
365
A
THR
366
n
383
THR
366
A
ALA
367
n
384
ALA
367
A
GLY
368
n
385
GLY
368
A
HIS
369
n
386
HIS
369
A
PRO
370
n
387
PRO
370
A
LEU
371
n
388
LEU
371
A
ALA
372
n
389
ALA
372
A
ARG
373
n
390
ARG
373
A
LEU
374
n
391
LEU
374
A
LEU
375
n
392
LEU
375
A
ARG
376
n
393
ARG
376
A
ASP
377
n
394
ASP
377
A
VAL
378
n
395
VAL
378
A
GLN
379
n
396
GLN
379
A
ALA
380
n
397
ALA
380
A
GLY
381
n
398
GLY
381
A
ARG
382
n
399
ARG
382
A
PHE
383
n
400
PHE
383
A
MET
384
n
401
MET
384
A
GLN
385
n
402
GLN
385
A
PRO
386
n
403
PRO
386
A
TYR
387
n
404
TYR
387
A
ALA
388
n
405
ALA
388
A
TYR
389
n
406
TYR
389
A
VAL
390
n
407
VAL
390
A
ASP
391
n
408
ASP
391
A
ALA
392
n
409
ALA
392
A
VAL
393
n
410
VAL
393
A
ASP
394
n
411
ASP
394
A
PHE
395
n
412
PHE
395
A
LEU
396
n
413
LEU
396
A
SER
397
n
414
SER
397
A
ALA
398
n
415
ALA
398
A
GLN
399
n
416
GLN
399
A
ALA
400
n
417
ALA
400
A
LEU
401
n
418
LEU
401
A
GLY
402
n
419
GLY
402
A
ILE
403
n
420
ILE
403
A
GLU
404
n
421
GLU
404
A
ARG
405
n
422
ARG
405
A
ASP
406
n
423
ASP
406
A
ASN
407
n
424
ASN
407
A
ASN
408
n
425
ASN
408
A
TYR
409
n
426
TYR
409
A
MET
410
n
427
MET
410
A
SER
411
n
428
SER
411
A
THR
412
n
429
THR
412
A
TRP
413
n
430
TRP
413
A
ALA
414
n
431
ALA
414
A
LYS
415
n
432
LYS
415
A
n
433
416
A
n
434
417
A
n
435
418
A
n
436
419
A
n
437
420
A
n
438
421
A
n
439
422
A
n
440
423
A
n
441
424
A
n
442
425
A
n
443
426
A
n
444
427
A
n
445
428
A
n
446
429
A
n
447
430
A
n
448
431
A
n
449
432
A
n
450
433
A
n
451
434
A
n
452
435
A
n
453
436
A
n
454
437
A
author_defined_assembly
1
monomeric
software_defined_assembly
PISA
4
tetrameric
software_defined_assembly
PISA
2
dimeric
software_defined_assembly
PISA
2
dimeric
15460
-99
53290
4500
-25
29880
4430
-25
29950
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_555
-x,-y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_555
-x,y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_555
x,-y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
N
CYS
140
A
N
CYS
157
A
O
HIS
178
A
O
HIS
195
A
N
ILE
181
A
N
ILE
198
A
O
PRO
197
A
O
PRO
214
A
O
ALA
195
A
O
ALA
212
A
N
ALA
183
A
N
ALA
200
A
O
ARG
184
A
O
ARG
201
A
N
LEU
153
A
N
LEU
170
A
N
ARG
154
A
N
ARG
171
A
O
LEU
162
A
O
LEU
179
A
N
TRP
161
A
N
TRP
178
A
O
ILE
232
A
O
ILE
249
A
O
VAL
226
A
O
VAL
243
A
N
THR
207
A
N
THR
224
A
N
CYS
140
A
N
CYS
157
A
O
HIS
178
A
O
HIS
195
A
N
ILE
181
A
N
ILE
198
A
O
PRO
197
A
O
PRO
214
A
N
LEU
194
A
N
LEU
211
A
O
ARG
240
A
O
ARG
257
1
A
C5'
FMN
502
C
C5'
FMN
1
1
N
1
A
O5'
FMN
502
C
O5'
FMN
1
1
N
1
A
P
FMN
502
C
P
FMN
1
1
N
1
A
O1P
FMN
502
C
O1P
FMN
1
1
N
1
A
O2P
FMN
502
C
O2P
FMN
1
1
N
1
A
O3P
FMN
502
C
O3P
FMN
1
1
N
1
A
HIS
-16
A
HIS
1
1
Y
1
A
HIS
-15
A
HIS
2
1
Y
1
A
HIS
-14
A
HIS
3
1
Y
1
A
HIS
-13
A
HIS
4
1
Y
1
A
HIS
-12
A
HIS
5
1
Y
1
A
HIS
-11
A
HIS
6
1
Y
1
A
SER
-10
A
SER
7
1
Y
1
A
SER
-9
A
SER
8
1
Y
1
A
GLY
-8
A
GLY
9
1
Y
1
A
GLU
-7
A
GLU
10
1
Y
1
A
ASN
-6
A
ASN
11
1
Y
1
A
LEU
-5
A
LEU
12
1
Y
1
A
TYR
-4
A
TYR
13
1
Y
1
A
GLU
-3
A
GLU
14
1
Y
1
A
GLN
-2
A
GLN
15
1
Y
1
A
GLY
-1
A
GLY
16
1
Y
1
A
HIS
0
A
HIS
17
1
Y
1
A
MET
1
A
MET
18
1
Y
1
A
PRO
2
A
PRO
19
1
Y
1
A
PRO
3
A
PRO
20
1
Y
1
A
TRP
4
A
TRP
21
1
Y
1
A
THR
5
A
THR
22
1
Y
1
A
ALA
6
A
ALA
23
1
Y
1
A
ARG
7
A
ARG
24
1
Y
1
A
GLN
8
A
GLN
25
1
Y
1
A
ARG
416
A
ARG
433
1
Y
1
A
SER
417
A
SER
434
1
Y
1
A
GLY
418
A
GLY
435
1
Y
1
A
GLY
419
A
GLY
436
1
Y
1
A
ASN
420
A
ASN
437
1
Y
1
A
GLY
421
A
GLY
438
1
Y
1
A
LYS
422
A
LYS
439
1
Y
1
A
SER
423
A
SER
440
1
Y
1
A
ALA
424
A
ALA
441
1
Y
1
A
ASP
425
A
ASP
442
1
Y
1
A
ALA
426
A
ALA
443
1
Y
1
A
ALA
427
A
ALA
444
1
Y
1
A
GLY
428
A
GLY
445
1
Y
1
A
PRO
429
A
PRO
446
1
Y
1
A
ARG
430
A
ARG
447
1
Y
1
A
ARG
431
A
ARG
448
1
Y
1
A
PRO
432
A
PRO
449
1
Y
1
A
THR
433
A
THR
450
1
Y
1
A
PRO
434
A
PRO
451
1
Y
1
A
THR
435
A
THR
452
1
Y
1
A
SER
436
A
SER
453
1
Y
1
A
ARG
437
A
ARG
454
1
Y
1
5.57
0.90
118.30
123.87
A
A
A
CB
CG
OD1
ASP
ASP
ASP
156
156
156
N
1
8.09
0.50
120.30
128.39
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
166
166
166
N
1
-6.07
0.50
120.30
114.23
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
166
166
166
N
1
3.38
0.50
120.30
123.68
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
282
282
282
N
1
3.44
0.50
120.30
123.74
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
306
306
306
N
1
-3.93
0.50
120.30
116.37
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
306
306
306
N
1
5.70
0.90
118.30
124.00
A
A
A
CB
CG
OD2
ASP
ASP
ASP
326
326
326
N
1
-12.62
1.60
100.20
87.58
A
A
A
CG
SD
CE
MET
MET
MET
384
384
384
N
1
A
ASP
118
-57.31
178.01
1
A
ALA
158
-157.51
26.66
1
A
LEU
169
66.13
70.39
1
A
THR
188
-100.53
-132.59
1
A
ASP
189
-142.28
-23.98
1
A
SER
196
-118.90
79.37
1
A
THR
222
-92.43
59.88
1
A
ARG
240
-104.11
-151.62
33.777
2.68
0.00
0.00
-0.93
0.00
-1.75
0.954
0.920
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.22518
0.17492
0.17742
2.098
76.31
1193
23596
5.1
89.93
4.307
0.117
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.223
0.188
0.80
0.80
1.40
PDB ENTRY 3M9V
MAXIMUM LIKELIHOOD
MASK
2.098
76.31
102
3188
61
0
3025
0.012
0.021
3157
2.269
1.990
4315
6.238
5.000
408
29.001
22.093
129
15.195
15.000
472
18.978
15.000
35
0.131
0.200
500
0.010
0.021
2400
1.218
1.500
2023
2.078
2.000
3226
3.124
3.000
1134
4.839
4.500
1089
0.207
0.180
2.152
67
1465
20
79.58
2.098
76.31
4KCF
23596
23596
0.069
1
5.7
90.4
2.098
2.18
17.5
2209
0.11
1
3.9
85.5
data collection
HKL-3000
phasing
PHASER
refinement
REFMAC
5.5.0109
data reduction
HKL-3000
data scaling
HKL-3000
X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose
1
N
N
2
N
N
3
N
N
4
N
N
A
THR
19
A
THR
36
HELX_P
A
ALA
31
A
ALA
48
1
1
13
A
HIS
32
A
HIS
49
HELX_P
A
THR
39
A
THR
56
1
2
8
A
THR
39
A
THR
56
HELX_P
A
GLY
47
A
GLY
64
1
3
9
A
PRO
50
A
PRO
67
HELX_P
A
ASP
60
A
ASP
77
1
4
11
A
GLY
61
A
GLY
78
HELX_P
A
ALA
65
A
ALA
82
5
5
5
A
PRO
68
A
PRO
85
HELX_P
A
GLY
72
A
GLY
89
5
6
5
A
ARG
78
A
ARG
95
HELX_P
A
ASP
93
A
ASP
110
1
7
16
A
ASP
93
A
ASP
110
HELX_P
A
GLY
117
A
GLY
134
1
8
25
A
ASP
118
A
ASP
135
HELX_P
A
ALA
134
A
ALA
151
1
9
17
A
MET
172
A
MET
189
HELX_P
A
GLY
176
A
GLY
193
5
10
5
A
PRO
233
A
PRO
250
HELX_P
A
ASP
235
A
ASP
252
5
11
3
A
ALA
249
A
ALA
266
HELX_P
A
SER
257
A
SER
274
1
12
9
A
SER
258
A
SER
275
HELX_P
A
SER
260
A
SER
277
5
13
3
A
VAL
261
A
VAL
278
HELX_P
A
ARG
282
A
ARG
299
1
14
22
A
GLN
288
A
GLN
305
HELX_P
A
ASP
322
A
ASP
339
1
15
35
A
ASP
326
A
ASP
343
HELX_P
A
GLY
361
A
GLY
378
1
16
36
A
GLY
362
A
GLY
379
HELX_P
A
THR
366
A
THR
383
5
17
5
A
HIS
369
A
HIS
386
HELX_P
A
VAL
378
A
VAL
395
1
18
10
A
GLN
379
A
GLN
396
HELX_P
A
MET
384
A
MET
401
5
19
6
A
ALA
388
A
ALA
405
HELX_P
A
LEU
401
A
LEU
418
1
20
14
A
ASN
408
A
ASN
425
HELX_P
A
LYS
415
A
LYS
432
1
21
8
OXIDOREDUCTASE
KijD3, fatty acyl-CoA dehydrogenase family, kijanose, kijanimicin, FAD, Flavoprotein, Oxidoreductase, class D flavin containing monooxygenases, N-oxygenase, nucleotide linked sugar, dTDP-3-amino-2, 3, 6-trideoxy-4-keto-3-methyl-D-glucose, FMN
A
GLN
385
A
GLN
402
1
A
PRO
386
A
PRO
403
-1.66
A
PRO
386
A
PRO
403
1
A
TYR
387
A
TYR
404
-15.73
B3TMR1_9ACTO
UNP
1
1
B3TMR1
MPPWTARQDSTTGLYAPVTPAGRVLLDRLAAHLPRIRSTAAEHDRDGTFPTDTFDALRKDGLMGATVPAELGGLGVDRLY
DVAVALLAVARADASTALALHMQLSRGLTLGYEWRHGDERARTLAERILRGMVAGDAVVCSGIKDHHTAVTTLRPDGAGG
WLLSGRKTLVSMAPVGTHFVINARTDGTDGPPRLASPVVTRDTPGFTVLDNWDGLGMRASGTVDIVFDDCPIPADHVLMR
DPVGARNDAVLAGQTVSSVSVLGVYVGVAQAAYDTAVAALERRPEPPQAAALTLVAEIDSRLYALRATAGSALTAADALS
ADLSGDMDERGRQMMRHFQCAKLAVNRLAPEIVSDCLSLVGGASYTAGHPLARLLRDVQAGRFMQPYAYVDAVDFLSAQA
LGIERDNNYMSTWAKRSGGNGKSADAAGPRRPTPTSR
1
437
4KCF
1
437
B3TMR1
A
1
18
454
1
expression tag
HIS
-16
4KCF
A
B3TMR1
UNP
1
1
expression tag
HIS
-15
4KCF
A
B3TMR1
UNP
2
1
expression tag
HIS
-14
4KCF
A
B3TMR1
UNP
3
1
expression tag
HIS
-13
4KCF
A
B3TMR1
UNP
4
1
expression tag
HIS
-12
4KCF
A
B3TMR1
UNP
5
1
expression tag
HIS
-11
4KCF
A
B3TMR1
UNP
6
1
expression tag
SER
-10
4KCF
A
B3TMR1
UNP
7
1
expression tag
SER
-9
4KCF
A
B3TMR1
UNP
8
1
expression tag
GLY
-8
4KCF
A
B3TMR1
UNP
9
1
expression tag
GLU
-7
4KCF
A
B3TMR1
UNP
10
1
expression tag
ASN
-6
4KCF
A
B3TMR1
UNP
11
1
expression tag
LEU
-5
4KCF
A
B3TMR1
UNP
12
1
expression tag
TYR
-4
4KCF
A
B3TMR1
UNP
13
1
expression tag
GLU
-3
4KCF
A
B3TMR1
UNP
14
1
expression tag
GLN
-2
4KCF
A
B3TMR1
UNP
15
1
expression tag
GLY
-1
4KCF
A
B3TMR1
UNP
16
1
expression tag
HIS
0
4KCF
A
B3TMR1
UNP
17
8
4
parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
VAL
139
A
VAL
156
A
GLY
142
A
GLY
159
A
HIS
178
A
HIS
195
A
ILE
181
A
ILE
198
A
ARG
193
A
ARG
210
A
THR
200
A
THR
217
A
ALA
183
A
ALA
200
A
THR
185
A
THR
202
A
THR
152
A
THR
169
A
PRO
155
A
PRO
172
A
TRP
161
A
TRP
178
A
VAL
170
A
VAL
187
A
VAL
223
A
VAL
240
A
ILE
232
A
ILE
249
A
PHE
206
A
PHE
223
A
VAL
208
A
VAL
225
A
VAL
139
A
VAL
156
A
GLY
142
A
GLY
159
A
HIS
178
A
HIS
195
A
ILE
181
A
ILE
198
A
ARG
193
A
ARG
210
A
THR
200
A
THR
217
A
VAL
237
A
VAL
254
A
PRO
242
A
PRO
259
BINDING SITE FOR RESIDUE AKM A 501
A
AKM
501
Software
27
BINDING SITE FOR RESIDUE FMN A 502
A
FMN
502
Software
15
A
HIS
101
A
HIS
118
27
1_555
A
MET
102
A
MET
119
27
1_555
A
SER
105
A
SER
122
27
1_555
A
ARG
106
A
ARG
123
27
1_555
A
THR
109
A
THR
126
27
1_555
A
TYR
112
A
TYR
129
27
1_555
A
GLU
113
A
GLU
130
27
1_555
A
SER
141
A
SER
158
27
1_555
A
ILE
143
A
ILE
160
27
1_555
A
ARG
240
A
ARG
257
27
1_555
A
ALA
252
A
ALA
269
27
1_555
A
GLY
253
A
GLY
270
27
1_555
A
GLN
254
A
GLN
271
27
1_555
A
VAL
256
A
VAL
273
27
1_555
A
SER
257
A
SER
274
27
1_555
A
SER
258
A
SER
275
27
1_555
A
ARG
330
A
ARG
347
27
1_555
A
MET
410
A
MET
427
27
1_555
A
FMN
502
C
FMN
27
1_555
A
HOH
621
D
HOH
27
1_555
A
HOH
635
D
HOH
27
1_555
A
HOH
646
D
HOH
27
1_555
A
HOH
647
D
HOH
27
1_555
A
HOH
670
D
HOH
27
1_555
A
HOH
684
D
HOH
27
1_555
A
HOH
687
D
HOH
27
1_555
A
HOH
699
D
HOH
27
1_555
A
MET
102
A
MET
119
15
1_555
A
SER
141
A
SER
158
15
1_555
A
ILE
143
A
ILE
160
15
1_555
A
LYS
144
A
LYS
161
15
1_555
A
LEU
169
A
LEU
186
15
1_555
A
SER
171
A
SER
188
15
1_555
A
THR
222
A
THR
239
15
1_555
A
PHE
383
A
PHE
400
15
1_555
A
MET
384
A
MET
401
15
1_555
A
GLN
385
A
GLN
402
15
1_555
A
TRP
413
A
TRP
430
15
1_555
A
AKM
501
B
AKM
15
1_555
A
HOH
624
D
HOH
15
1_555
A
HOH
666
D
HOH
15
1_555
A
HOH
699
D
HOH
15
1_555
23
I 2 2 2