0.013722
0.000000
0.000000
0.000000
0.010601
0.000000
0.000000
0.000000
0.016059
0.000000
0.000000
0.000000
Basarab, G.S.
Manchester, J.I.
Bist, S.
Boriack-Sjodin, P.A.
Dangel, B.
Illingsworth, R.
Uria-Nickelsen, M.
Sherer, B.A.
Sriram, S.
Eakin, A.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
72.875
94.333
62.270
C18 H14 F3 N5 O3 S
437.396
6'-[(ethylcarbamoyl)amino]-4'-[4-(trifluoromethyl)-1,3-thiazol-2-yl]-3,3'-bipyridine-5-carboxylic acid
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
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
C
N
2
N
C
N
3
N
O
N
4
N
N
Y
5
N
C
Y
6
N
C
Y
7
N
C
Y
8
N
C
Y
9
N
C
Y
10
N
C
Y
11
N
C
Y
12
N
C
Y
13
N
C
N
14
N
C
Y
15
N
C
Y
16
N
N
Y
17
N
C
N
18
N
C
N
19
N
N
N
20
N
C
Y
21
N
N
Y
22
N
N
Y
23
N
C
N
24
N
O
N
25
N
O
Y
26
N
C
Y
27
N
S
N
28
N
F
N
29
N
F
N
30
N
F
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
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
N
N
46
S
C
N
47
N
C
N
48
N
O
N
49
N
C
N
50
N
O
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
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
C
N
65
N
N
N
66
N
C
N
67
N
N
N
68
N
N
N
69
N
O
N
70
N
H
N
71
N
H
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
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
N
N
86
S
C
N
87
N
C
N
88
N
O
N
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
O
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
N
N
103
S
C
N
104
N
C
N
105
N
O
N
106
N
C
N
107
N
C
N
108
N
O
N
109
N
O
N
110
N
O
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
N
N
119
S
C
N
120
N
C
N
121
N
O
N
122
N
C
N
123
N
C
N
124
N
C
N
125
N
O
N
126
N
N
N
127
N
O
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
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
N
N
139
S
C
N
140
N
C
N
141
N
O
N
142
N
C
N
143
N
C
N
144
N
C
N
145
N
O
N
146
N
O
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
N
N
158
N
C
N
159
N
C
N
160
N
O
N
161
N
O
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
N
N
168
S
C
N
169
N
C
N
170
N
O
N
171
N
C
Y
172
N
C
Y
173
N
N
Y
174
N
C
Y
175
N
C
Y
176
N
N
N
177
N
O
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
O
N
189
N
H
N
190
N
H
N
191
N
N
N
192
S
C
N
193
N
C
N
194
N
O
N
195
S
C
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
O
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
N
N
214
S
C
N
215
N
C
N
216
N
O
N
217
N
C
N
218
N
C
N
219
N
C
N
220
N
C
N
221
N
O
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
N
N
236
S
C
N
237
N
C
N
238
N
O
N
239
N
C
N
240
N
C
N
241
N
C
N
242
N
C
N
243
N
N
N
244
N
O
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
N
N
261
S
C
N
262
N
C
N
263
N
O
N
264
N
C
N
265
N
C
N
266
N
S
N
267
N
C
N
268
N
O
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
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
Y
285
N
C
Y
286
N
C
Y
287
N
C
Y
288
N
C
Y
289
N
C
Y
290
N
C
N
291
N
O
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
H
N
301
N
H
N
302
N
H
N
303
N
N
N
304
S
C
N
305
N
C
N
306
N
O
N
307
N
C
N
308
N
C
N
309
N
C
N
310
N
O
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
N
N
321
S
C
N
322
N
C
N
323
N
O
N
324
N
C
N
325
N
O
N
326
N
O
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
N
N
335
S
C
N
336
N
C
N
337
N
O
N
338
R
C
N
339
N
O
N
340
N
C
N
341
N
O
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
N
N
352
S
C
N
353
N
C
N
354
N
O
N
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
N
Y
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
C
Y
364
N
C
N
365
N
O
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
N
N
379
S
C
N
380
N
C
N
381
N
O
N
382
N
C
Y
383
N
C
Y
384
N
C
Y
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
N
389
N
O
N
390
N
O
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
N
N
403
S
C
N
404
N
C
N
405
N
O
N
406
N
C
N
407
N
C
N
408
N
C
N
409
N
O
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
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
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
doub
N
5
N
sing
N
6
N
sing
Y
7
N
doub
Y
8
N
sing
Y
9
N
sing
Y
10
N
doub
Y
11
N
sing
Y
12
N
sing
N
13
N
sing
Y
14
N
doub
Y
15
N
sing
Y
16
N
doub
N
17
N
sing
Y
18
N
doub
N
19
N
doub
Y
20
N
doub
Y
21
N
sing
Y
22
N
sing
Y
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
Y
27
N
doub
Y
28
N
doub
N
29
N
sing
N
30
N
sing
N
31
N
sing
Y
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
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
doub
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
doub
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
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
doub
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
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
doub
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
doub
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
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
doub
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
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
doub
N
131
N
sing
N
132
N
sing
N
133
N
sing
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
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
doub
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
doub
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
Y
173
N
sing
Y
174
N
doub
Y
175
N
doub
N
176
N
sing
Y
177
N
sing
N
178
N
sing
Y
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
doub
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
sing
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
sing
N
211
N
sing
N
212
N
doub
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
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
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
doub
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
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
sing
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
sing
N
257
N
doub
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
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
doub
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
Y
281
N
doub
Y
282
N
sing
Y
283
N
sing
N
284
N
sing
Y
285
N
doub
N
286
N
sing
Y
287
N
doub
N
288
N
sing
Y
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
doub
N
300
N
sing
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
doub
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
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
doub
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
Y
350
N
doub
Y
351
N
sing
Y
352
N
sing
N
353
N
sing
Y
354
N
doub
Y
355
N
sing
Y
356
N
sing
N
357
N
sing
Y
358
N
sing
Y
359
N
doub
N
360
N
sing
Y
361
N
doub
N
362
N
sing
Y
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
doub
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
Y
378
N
doub
Y
379
N
sing
Y
380
N
sing
N
381
N
sing
Y
382
N
doub
N
383
N
sing
Y
384
N
doub
N
385
N
sing
Y
386
N
sing
N
387
N
sing
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
doub
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
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
US
J.Med.Chem.
JMCMAR
0151
0022-2623
56
8712
8735
10.1021/jm401208b
24098982
Fragment-to-Hit-to-Lead Discovery of a Novel Pyridylurea Scaffold of ATP Competitive Dual Targeting Type II Topoisomerase Inhibiting Antibacterial Agents.
2013
10.2210/pdb4lp0/pdb
pdb_00004lp0
100
1
monochromator
CCD
2007-05-29
RAYONIX MX-225
Diamond(111) crystal
SINGLE WAVELENGTH
M
x-ray
1
1.000
1.0
31-ID
APS
1.000
SYNCHROTRON
APS BEAMLINE 31-ID
24600.723
Topoisomerase IV subunit B
5.99.1.-
ATPase domain, UNP residues 1-226
1
man
polymer
437.396
6'-[(ethylcarbamoyl)amino]-4'-[4-(trifluoromethyl)-1,3-thiazol-2-yl]-3,3'-bipyridine-5-carboxylic acid
1
syn
non-polymer
18.015
water
107
nat
water
no
no
MSKKEININNYNDDAIQVLEGLDAVRKRPGMYIGSTDGAGLHHLVWEIVDNAVDEALSGFGDRIDVTINKDGSLTVQDHG
RGMPTGMHAMGIPTVEVIFTILHAGGKFGQGGYKTSGGLHGVGSSVVNALSSWLEVEITRDGAVYKQRFENGGKPVTTLK
KIGTALKSKTGTKVTFMPDATIFSTTDFKYNTISERLNESAFLLKNVTLSLTDKRTDEAIEFHYEN
MSKKEININNYNDDAIQVLEGLDAVRKRPGMYIGSTDGAGLHHLVWEIVDNAVDEALSGFGDRIDVTINKDGSLTVQDHG
RGMPTGMHAMGIPTVEVIFTILHAGGKFGQGGYKTSGGLHGVGSSVVNALSSWLEVEITRDGAVYKQRFENGGKPVTTLK
KIGTALKSKTGTKVTFMPDATIFSTTDFKYNTISERLNESAFLLKNVTLSLTDKRTDEAIEFHYEN
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
ATCC BAA-255 / R6
sample
parE, spr0756
171101
Streptococcus pneumoniae
469008
Escherichia coli
BL21(DE3)
plasmid
1
2.18
43.45
VAPOR DIFFUSION, HANGING DROP
7.0
18-25% Peg4000, 0.2M Ammonium Acetate, 0.1M MIB pH 7, inhibitor soak, temperature 293K, VAPOR DIFFUSION, HANGING DROP
293
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
1
0
2013-11-13
1
1
2014-01-15
1
2
2024-02-28
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2013-07-14
REL
REL
1YM
6'-[(ethylcarbamoyl)amino]-4'-[4-(trifluoromethyl)-1,3-thiazol-2-yl]-3,3'-bipyridine-5-carboxylic acid
HOH
water
1YM
1
2
1YM
1YM
301
A
HOH
1
3
HOH
HOH
401
A
HOH
2
3
HOH
HOH
402
A
HOH
3
3
HOH
HOH
403
A
HOH
4
3
HOH
HOH
404
A
HOH
5
3
HOH
HOH
405
A
HOH
6
3
HOH
HOH
406
A
HOH
7
3
HOH
HOH
407
A
HOH
8
3
HOH
HOH
408
A
HOH
9
3
HOH
HOH
409
A
HOH
10
3
HOH
HOH
410
A
HOH
11
3
HOH
HOH
411
A
HOH
12
3
HOH
HOH
412
A
HOH
13
3
HOH
HOH
413
A
HOH
14
3
HOH
HOH
414
A
HOH
15
3
HOH
HOH
415
A
HOH
16
3
HOH
HOH
416
A
HOH
17
3
HOH
HOH
417
A
HOH
19
3
HOH
HOH
418
A
HOH
20
3
HOH
HOH
419
A
HOH
21
3
HOH
HOH
420
A
HOH
22
3
HOH
HOH
421
A
HOH
24
3
HOH
HOH
422
A
HOH
25
3
HOH
HOH
423
A
HOH
26
3
HOH
HOH
424
A
HOH
27
3
HOH
HOH
425
A
HOH
28
3
HOH
HOH
426
A
HOH
29
3
HOH
HOH
427
A
HOH
30
3
HOH
HOH
428
A
HOH
31
3
HOH
HOH
429
A
HOH
32
3
HOH
HOH
430
A
HOH
33
3
HOH
HOH
431
A
HOH
34
3
HOH
HOH
432
A
HOH
35
3
HOH
HOH
433
A
HOH
36
3
HOH
HOH
434
A
HOH
37
3
HOH
HOH
435
A
HOH
38
3
HOH
HOH
436
A
HOH
39
3
HOH
HOH
437
A
HOH
40
3
HOH
HOH
438
A
HOH
41
3
HOH
HOH
439
A
HOH
42
3
HOH
HOH
440
A
HOH
43
3
HOH
HOH
441
A
HOH
44
3
HOH
HOH
442
A
HOH
47
3
HOH
HOH
443
A
HOH
49
3
HOH
HOH
444
A
HOH
50
3
HOH
HOH
445
A
HOH
51
3
HOH
HOH
446
A
HOH
53
3
HOH
HOH
447
A
HOH
54
3
HOH
HOH
448
A
HOH
56
3
HOH
HOH
449
A
HOH
57
3
HOH
HOH
450
A
HOH
58
3
HOH
HOH
451
A
HOH
59
3
HOH
HOH
452
A
HOH
62
3
HOH
HOH
453
A
HOH
64
3
HOH
HOH
454
A
HOH
65
3
HOH
HOH
455
A
HOH
68
3
HOH
HOH
456
A
HOH
69
3
HOH
HOH
457
A
HOH
70
3
HOH
HOH
458
A
HOH
71
3
HOH
HOH
459
A
HOH
74
3
HOH
HOH
460
A
HOH
75
3
HOH
HOH
461
A
HOH
76
3
HOH
HOH
462
A
HOH
80
3
HOH
HOH
463
A
HOH
81
3
HOH
HOH
464
A
HOH
82
3
HOH
HOH
465
A
HOH
83
3
HOH
HOH
466
A
HOH
84
3
HOH
HOH
467
A
HOH
85
3
HOH
HOH
468
A
HOH
86
3
HOH
HOH
469
A
HOH
87
3
HOH
HOH
470
A
HOH
88
3
HOH
HOH
471
A
HOH
89
3
HOH
HOH
472
A
HOH
90
3
HOH
HOH
473
A
HOH
91
3
HOH
HOH
474
A
HOH
93
3
HOH
HOH
475
A
HOH
94
3
HOH
HOH
476
A
HOH
96
3
HOH
HOH
477
A
HOH
98
3
HOH
HOH
478
A
HOH
99
3
HOH
HOH
479
A
HOH
100
3
HOH
HOH
480
A
HOH
102
3
HOH
HOH
481
A
HOH
104
3
HOH
HOH
482
A
HOH
105
3
HOH
HOH
483
A
HOH
106
3
HOH
HOH
484
A
HOH
115
3
HOH
HOH
485
A
HOH
116
3
HOH
HOH
486
A
HOH
124
3
HOH
HOH
487
A
HOH
127
3
HOH
HOH
488
A
HOH
128
3
HOH
HOH
489
A
HOH
129
3
HOH
HOH
490
A
HOH
132
3
HOH
HOH
491
A
HOH
134
3
HOH
HOH
492
A
HOH
135
3
HOH
HOH
493
A
HOH
136
3
HOH
HOH
494
A
HOH
137
3
HOH
HOH
495
A
HOH
138
3
HOH
HOH
496
A
HOH
139
3
HOH
HOH
497
A
HOH
140
3
HOH
HOH
498
A
HOH
141
3
HOH
HOH
499
A
HOH
142
3
HOH
HOH
500
A
HOH
143
3
HOH
HOH
501
A
HOH
144
3
HOH
HOH
502
A
HOH
145
3
HOH
HOH
503
A
HOH
146
3
HOH
HOH
504
A
HOH
147
3
HOH
HOH
505
A
HOH
148
3
HOH
HOH
506
A
HOH
149
3
HOH
HOH
507
A
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
n
6
6
A
n
7
7
A
n
8
8
A
n
9
9
A
n
10
10
A
n
11
11
A
n
12
12
A
n
13
13
A
n
14
14
A
n
15
15
A
n
16
16
A
GLN
17
n
17
GLN
17
A
VAL
18
n
18
VAL
18
A
LEU
19
n
19
LEU
19
A
GLU
20
n
20
GLU
20
A
GLY
21
n
21
GLY
21
A
LEU
22
n
22
LEU
22
A
ASP
23
n
23
ASP
23
A
ALA
24
n
24
ALA
24
A
VAL
25
n
25
VAL
25
A
ARG
26
n
26
ARG
26
A
LYS
27
n
27
LYS
27
A
ARG
28
n
28
ARG
28
A
PRO
29
n
29
PRO
29
A
GLY
30
n
30
GLY
30
A
MET
31
n
31
MET
31
A
TYR
32
n
32
TYR
32
A
ILE
33
n
33
ILE
33
A
GLY
34
n
34
GLY
34
A
SER
35
n
35
SER
35
A
THR
36
n
36
THR
36
A
ASP
37
n
37
ASP
37
A
GLY
38
n
38
GLY
38
A
ALA
39
n
39
ALA
39
A
GLY
40
n
40
GLY
40
A
LEU
41
n
41
LEU
41
A
HIS
42
n
42
HIS
42
A
HIS
43
n
43
HIS
43
A
LEU
44
n
44
LEU
44
A
VAL
45
n
45
VAL
45
A
TRP
46
n
46
TRP
46
A
GLU
47
n
47
GLU
47
A
ILE
48
n
48
ILE
48
A
VAL
49
n
49
VAL
49
A
ASP
50
n
50
ASP
50
A
ASN
51
n
51
ASN
51
A
ALA
52
n
52
ALA
52
A
VAL
53
n
53
VAL
53
A
ASP
54
n
54
ASP
54
A
GLU
55
n
55
GLU
55
A
ALA
56
n
56
ALA
56
A
LEU
57
n
57
LEU
57
A
SER
58
n
58
SER
58
A
GLY
59
n
59
GLY
59
A
PHE
60
n
60
PHE
60
A
GLY
61
n
61
GLY
61
A
ASP
62
n
62
ASP
62
A
ARG
63
n
63
ARG
63
A
ILE
64
n
64
ILE
64
A
ASP
65
n
65
ASP
65
A
VAL
66
n
66
VAL
66
A
THR
67
n
67
THR
67
A
ILE
68
n
68
ILE
68
A
ASN
69
n
69
ASN
69
A
LYS
70
n
70
LYS
70
A
ASP
71
n
71
ASP
71
A
GLY
72
n
72
GLY
72
A
SER
73
n
73
SER
73
A
LEU
74
n
74
LEU
74
A
THR
75
n
75
THR
75
A
VAL
76
n
76
VAL
76
A
GLN
77
n
77
GLN
77
A
ASP
78
n
78
ASP
78
A
HIS
79
n
79
HIS
79
A
GLY
80
n
80
GLY
80
A
ARG
81
n
81
ARG
81
A
GLY
82
n
82
GLY
82
A
MET
83
n
83
MET
83
A
PRO
84
n
84
PRO
84
A
THR
85
n
85
THR
85
A
GLY
86
n
86
GLY
86
A
MET
87
n
87
MET
87
A
HIS
88
n
88
HIS
88
A
ALA
89
n
89
ALA
89
A
MET
90
n
90
MET
90
A
GLY
91
n
91
GLY
91
A
ILE
92
n
92
ILE
92
A
PRO
93
n
93
PRO
93
A
THR
94
n
94
THR
94
A
VAL
95
n
95
VAL
95
A
GLU
96
n
96
GLU
96
A
VAL
97
n
97
VAL
97
A
ILE
98
n
98
ILE
98
A
PHE
99
n
99
PHE
99
A
THR
100
n
100
THR
100
A
ILE
101
n
101
ILE
101
A
LEU
102
n
102
LEU
102
A
HIS
103
n
103
HIS
103
A
n
104
104
A
n
105
105
A
n
106
106
A
n
107
107
A
n
108
108
A
n
109
109
A
n
110
110
A
n
111
111
A
n
112
112
A
n
113
113
A
n
114
114
A
n
115
115
A
n
116
116
A
n
117
117
A
n
118
118
A
n
119
119
A
n
120
120
A
n
121
121
A
VAL
122
n
122
VAL
122
A
GLY
123
n
123
GLY
123
A
SER
124
n
124
SER
124
A
SER
125
n
125
SER
125
A
VAL
126
n
126
VAL
126
A
VAL
127
n
127
VAL
127
A
ASN
128
n
128
ASN
128
A
ALA
129
n
129
ALA
129
A
LEU
130
n
130
LEU
130
A
SER
131
n
131
SER
131
A
SER
132
n
132
SER
132
A
TRP
133
n
133
TRP
133
A
LEU
134
n
134
LEU
134
A
GLU
135
n
135
GLU
135
A
VAL
136
n
136
VAL
136
A
GLU
137
n
137
GLU
137
A
ILE
138
n
138
ILE
138
A
THR
139
n
139
THR
139
A
ARG
140
n
140
ARG
140
A
ASP
141
n
141
ASP
141
A
GLY
142
n
142
GLY
142
A
ALA
143
n
143
ALA
143
A
VAL
144
n
144
VAL
144
A
TYR
145
n
145
TYR
145
A
LYS
146
n
146
LYS
146
A
GLN
147
n
147
GLN
147
A
ARG
148
n
148
ARG
148
A
PHE
149
n
149
PHE
149
A
GLU
150
n
150
GLU
150
A
ASN
151
n
151
ASN
151
A
GLY
152
n
152
GLY
152
A
GLY
153
n
153
GLY
153
A
LYS
154
n
154
LYS
154
A
PRO
155
n
155
PRO
155
A
VAL
156
n
156
VAL
156
A
THR
157
n
157
THR
157
A
THR
158
n
158
THR
158
A
LEU
159
n
159
LEU
159
A
LYS
160
n
160
LYS
160
A
LYS
161
n
161
LYS
161
A
ILE
162
n
162
ILE
162
A
GLY
163
n
163
GLY
163
A
THR
164
n
164
THR
164
A
ALA
165
n
165
ALA
165
A
LEU
166
n
166
LEU
166
A
LYS
167
n
167
LYS
167
A
SER
168
n
168
SER
168
A
LYS
169
n
169
LYS
169
A
THR
170
n
170
THR
170
A
GLY
171
n
171
GLY
171
A
THR
172
n
172
THR
172
A
LYS
173
n
173
LYS
173
A
VAL
174
n
174
VAL
174
A
THR
175
n
175
THR
175
A
PHE
176
n
176
PHE
176
A
MET
177
n
177
MET
177
A
PRO
178
n
178
PRO
178
A
ASP
179
n
179
ASP
179
A
ALA
180
n
180
ALA
180
A
THR
181
n
181
THR
181
A
ILE
182
n
182
ILE
182
A
PHE
183
n
183
PHE
183
A
SER
184
n
184
SER
184
A
THR
185
n
185
THR
185
A
THR
186
n
186
THR
186
A
ASP
187
n
187
ASP
187
A
PHE
188
n
188
PHE
188
A
LYS
189
n
189
LYS
189
A
TYR
190
n
190
TYR
190
A
ASN
191
n
191
ASN
191
A
THR
192
n
192
THR
192
A
ILE
193
n
193
ILE
193
A
SER
194
n
194
SER
194
A
GLU
195
n
195
GLU
195
A
ARG
196
n
196
ARG
196
A
LEU
197
n
197
LEU
197
A
ASN
198
n
198
ASN
198
A
GLU
199
n
199
GLU
199
A
SER
200
n
200
SER
200
A
ALA
201
n
201
ALA
201
A
PHE
202
n
202
PHE
202
A
LEU
203
n
203
LEU
203
A
LEU
204
n
204
LEU
204
A
LYS
205
n
205
LYS
205
A
ASN
206
n
206
ASN
206
A
VAL
207
n
207
VAL
207
A
THR
208
n
208
THR
208
A
LEU
209
n
209
LEU
209
A
SER
210
n
210
SER
210
A
LEU
211
n
211
LEU
211
A
THR
212
n
212
THR
212
A
ASP
213
n
213
ASP
213
A
LYS
214
n
214
LYS
214
A
ARG
215
n
215
ARG
215
A
THR
216
n
216
THR
216
A
ASP
217
n
217
ASP
217
A
GLU
218
n
218
GLU
218
A
ALA
219
n
219
ALA
219
A
ILE
220
n
220
ILE
220
A
GLU
221
n
221
GLU
221
A
PHE
222
n
222
PHE
222
A
HIS
223
n
223
HIS
223
A
TYR
224
n
224
TYR
224
A
GLU
225
n
225
GLU
225
A
ASN
226
n
226
ASN
226
A
0.0927
-0.1831
0.0165
0.6931
-0.1921
0.5642
-0.0106
0.0095
-0.0092
-0.0107
-0.0511
-0.0265
0.0294
0.0443
0.0617
0.0050
-0.0001
0.0047
0.0244
0.0155
0.0236
refined
23.0820
32.0980
0.6350
X-RAY DIFFRACTION
A
17
A
226
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA
1
monomeric
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
A
O
LYS
154
A
O
LYS
154
A
N
GLU
150
A
N
GLU
150
A
N
VAL
144
A
N
VAL
144
A
O
ILE
162
A
O
ILE
162
A
O
LYS
154
A
O
LYS
154
A
N
GLU
150
A
N
GLU
150
A
O
TYR
145
A
O
TYR
145
A
N
ILE
138
A
N
ILE
138
A
N
GLU
137
A
N
GLU
137
A
O
LYS
173
A
O
LYS
173
A
O
THR
172
A
O
THR
172
A
N
ASP
78
A
N
ASP
78
A
O
GLN
77
A
O
GLN
77
A
N
ASP
65
A
N
ASP
65
A
N
ILE
68
A
N
ILE
68
A
O
THR
212
A
O
THR
212
A
N
LEU
211
A
N
LEU
211
A
O
ILE
220
A
O
ILE
220
1
A
MET
1
A
MET
1
1
Y
1
A
SER
2
A
SER
2
1
Y
1
A
LYS
3
A
LYS
3
1
Y
1
A
LYS
4
A
LYS
4
1
Y
1
A
GLU
5
A
GLU
5
1
Y
1
A
ILE
6
A
ILE
6
1
Y
1
A
ASN
7
A
ASN
7
1
Y
1
A
ILE
8
A
ILE
8
1
Y
1
A
ASN
9
A
ASN
9
1
Y
1
A
ASN
10
A
ASN
10
1
Y
1
A
TYR
11
A
TYR
11
1
Y
1
A
ASN
12
A
ASN
12
1
Y
1
A
ASP
13
A
ASP
13
1
Y
1
A
ASP
14
A
ASP
14
1
Y
1
A
ALA
15
A
ALA
15
1
Y
1
A
ILE
16
A
ILE
16
1
Y
1
A
ALA
104
A
ALA
104
1
Y
1
A
GLY
105
A
GLY
105
1
Y
1
A
GLY
106
A
GLY
106
1
Y
1
A
LYS
107
A
LYS
107
1
Y
1
A
PHE
108
A
PHE
108
1
Y
1
A
GLY
109
A
GLY
109
1
Y
1
A
GLN
110
A
GLN
110
1
Y
1
A
GLY
111
A
GLY
111
1
Y
1
A
GLY
112
A
GLY
112
1
Y
1
A
TYR
113
A
TYR
113
1
Y
1
A
LYS
114
A
LYS
114
1
Y
1
A
THR
115
A
THR
115
1
Y
1
A
SER
116
A
SER
116
1
Y
1
A
GLY
117
A
GLY
117
1
Y
1
A
GLY
118
A
GLY
118
1
Y
1
A
LEU
119
A
LEU
119
1
Y
1
A
HIS
120
A
HIS
120
1
Y
1
A
GLY
121
A
GLY
121
1
Y
1
4.23
0.50
120.30
124.53
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
26
26
26
N
1
6.36
0.90
118.30
124.66
A
A
A
CB
CG
OD1
ASP
ASP
ASP
50
50
50
N
1
-6.79
0.90
118.30
111.51
A
A
A
CB
CG
OD2
ASP
ASP
ASP
50
50
50
N
1
A
ASP
37
-97.93
-159.60
1
A
HIS
88
A
-87.76
-139.73
1
A
HIS
88
B
-99.54
-150.12
1
A
LYS
205
64.00
141.77
26.360
0.66
-0.00
0.00
-0.40
-0.00
-0.26
0.960
0.950
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.20197
0.16638
0.16816
1.95
57.67
788
15830
15042
5.0
99.50
1.000
0.500
6.263
0.094
0.1547
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.146
0.133
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
1.95
57.67
107
1617
30
0
1480
0.018
0.019
1573
0.005
0.020
1477
1.670
1.967
2135
0.825
3.000
3400
5.803
5.000
196
29.767
24.030
67
13.348
15.000
268
15.412
15.000
9
0.101
0.200
242
0.008
0.020
1782
0.001
0.020
349
2.298
2.069
781
2.299
2.064
780
3.028
3.071
978
3.226
2.462
792
0.253
0.210
2.005
60
1123
20
99.92
1.955
62.270
4LP0
15850
15850
0.0
0.0
0.084
1
16.300
7.100
99.800
0.386
1.950
2.060
2.000
0.386
1
7.300
100.000
0.265
2.060
2.190
2.800
0.265
1
7.300
100.000
0.229
2.190
2.340
3.200
0.229
1
7.100
100.000
0.178
2.340
2.520
4.100
0.178
1
7.300
99.900
0.127
2.520
2.760
5.700
0.127
1
7.300
99.900
0.092
2.760
3.090
7.900
0.092
1
7.200
99.800
0.060
3.090
3.570
11.600
0.060
1
7.000
99.700
0.047
3.570
4.370
13.900
0.047
1
6.800
99.700
0.040
4.370
6.180
14.800
0.040
1
6.700
99.800
0.038
6.180
62.270
15.300
0.038
1
6.000
95.800
data scaling
Phil R. Evans
pre@mrc-lmb.cam.ac.uk
2011/05/18
Fortran_77
http://www.ccp4.ac.uk/dist/html/scala.html
SCALA
other
3.3.20
phasing
Jorge Navaza
ccp4@ccp4.ac.uk
Fortran_77
http://www.ccp4.ac.uk/
AMoRE
program
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
deposit@deposit.rcsb.org
April 22, 2011
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.11
data scaling
XSCALE
Crystal structure of a topoisomerase ATP inhibitor
1
N
N
2
N
N
3
N
N
A
LEU
22
A
LEU
22
HELX_P
A
ARG
28
A
ARG
28
1
1
7
A
ARG
28
A
ARG
28
HELX_P
A
GLY
34
A
GLY
34
1
2
7
A
ASP
37
A
ASP
37
HELX_P
A
SER
58
A
SER
58
1
3
22
A
PRO
93
A
PRO
93
HELX_P
A
ILE
101
A
ILE
101
1
4
9
A
GLY
123
A
GLY
123
HELX_P
A
LEU
130
A
LEU
130
1
5
8
A
LYS
189
A
LYS
189
HELX_P
A
LYS
205
A
LYS
205
1
6
17
ISOMERASE/ISOMERASE INHIBITOR
protein-inhibitor complex, ATP binding, structure-based drug design, antimicrobial, virtual screen, ATPase domain, ISOMERASE-ISOMERASE INHIBITOR complex
Q8DQB5_STRR6
UNP
1
1
Q8DQB5
MSKKEININNYNDDAIQVLEGLDAVRKRPGMYIGSTDGAGLHHLVWEIVDNAVDEALSGFGDRIDVTINKDGSLTVQDHG
RGMPTGMHAMGIPTVEVIFTILHAGGKFGQGGYKTSGGLHGVGSSVVNALSSWLEVEITRDGAVYKQRFENGGKPVTTLK
KIGTALKSKTGTKVTFMPDATIFSTTDFKYNTISERLNESAFLLKNVTLSLTDKRTDEAIEFHYEN
1
226
4LP0
1
226
Q8DQB5
A
1
1
226
3
8
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
A
LYS
154
A
LYS
154
A
PRO
155
A
PRO
155
A
ALA
143
A
ALA
143
A
GLU
150
A
GLU
150
A
LYS
160
A
LYS
160
A
THR
164
A
THR
164
A
LYS
154
A
LYS
154
A
PRO
155
A
PRO
155
A
ALA
143
A
ALA
143
A
GLU
150
A
GLU
150
A
SER
131
A
SER
131
A
ARG
140
A
ARG
140
A
GLY
171
A
GLY
171
A
PRO
178
A
PRO
178
A
LEU
74
A
LEU
74
A
ASP
78
A
ASP
78
A
ARG
63
A
ARG
63
A
ILE
68
A
ILE
68
A
THR
208
A
THR
208
A
ASP
213
A
ASP
213
A
ALA
219
A
ALA
219
A
PHE
222
A
PHE
222
BINDING SITE FOR RESIDUE 1YM A 301
A
1YM
301
Software
12
A
ASN
51
A
ASN
51
12
1_555
A
GLU
55
A
GLU
55
12
1_555
A
VAL
76
A
VAL
76
12
1_555
A
ASP
78
A
ASP
78
12
1_555
A
ARG
81
A
ARG
81
12
1_555
A
GLY
82
A
GLY
82
12
1_555
A
MET
83
A
MET
83
12
1_555
A
PRO
84
A
PRO
84
12
1_555
A
ILE
98
A
ILE
98
12
1_555
A
THR
172
A
THR
172
12
1_555
A
HOH
404
C
HOH
12
1_555
A
HOH
507
C
HOH
12
1_555
20
C 2 2 21