0.019635
0.000000
0.000000
0.000000
0.017227
0.000000
0.000000
0.000000
0.016242
0.00000
0.00000
0.00000
Tyndall, J.D.
Pattenden, L.K.
Reid, R.C.
Hu, S.H.
Alewood, D.
Alewood, P.F.
Walsh, T.
Fairlie, D.P.
Martin, J.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
50.93
58.05
61.57
C4 H9 N O2
103.120
n
ALPHA-AMINOBUTYRIC ACID
L-peptide linking
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
C37 H51 N5 O7
677.830
(9S,12S)-9-(1-methylethyl)-N-[(8S,11S)-8-[(1S)-1-methylpropyl]-7,10-dioxo-2-oxa-6,9-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-11-yl]-7,10-dioxo-2-oxa-8,11-diazabicyclo[12.2.2]octadeca-1(16),14,17-triene-12-carboxamide
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
O4 S -2
96.063
SULFATE ION
non-polymer
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
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
C
N
7
N
O
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
N
N
18
S
C
N
19
N
C
N
20
N
O
N
21
N
C
N
22
N
O
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
N
N
31
S
C
N
32
N
C
N
33
N
O
N
34
N
C
N
35
N
C
N
36
N
C
N
37
N
N
N
38
N
C
N
39
N
N
N
40
N
N
N
41
N
O
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
N
N
58
S
C
N
59
N
C
N
60
N
O
N
61
N
C
N
62
N
C
N
63
N
O
N
64
N
N
N
65
N
O
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
O
N
81
N
O
N
82
N
O
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
N
N
91
R
C
N
92
N
C
N
93
N
O
N
94
N
C
N
95
N
S
N
96
N
O
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
C
N
105
N
C
N
106
S
C
N
107
N
C
N
108
S
C
N
109
N
N
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
O
N
114
N
N
N
115
N
C
N
116
N
C
N
117
N
C
N
118
N
O
Y
119
N
C
Y
120
N
C
Y
121
N
C
Y
122
N
C
Y
123
N
C
Y
124
N
C
N
125
N
C
N
126
S
C
N
127
N
N
N
128
N
C
N
129
N
O
N
130
S
C
N
131
N
C
Y
132
N
C
Y
133
N
C
Y
134
N
C
Y
135
N
C
Y
136
N
C
Y
137
N
C
N
138
N
O
N
139
N
C
N
140
N
C
N
141
N
C
N
142
N
C
N
143
N
C
N
144
N
O
N
145
N
N
N
146
S
C
N
147
N
C
N
148
N
C
N
149
N
C
N
150
N
C
N
151
N
O
N
152
N
N
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
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
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
N
N
205
S
C
N
206
N
C
N
207
N
O
N
208
N
C
N
209
N
C
N
210
N
C
N
211
N
O
N
212
N
N
N
213
N
O
N
214
N
H
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
N
N
225
S
C
N
226
N
C
N
227
N
O
N
228
N
C
N
229
N
C
N
230
N
C
N
231
N
O
N
232
N
O
N
233
N
O
N
234
N
H
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
N
N
244
N
C
N
245
N
C
N
246
N
O
N
247
N
O
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
N
N
254
S
C
N
255
N
C
N
256
N
O
N
257
N
C
Y
258
N
C
Y
259
N
N
Y
260
N
C
Y
261
N
C
Y
262
N
N
N
263
N
O
N
264
N
H
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
O
N
275
N
H
N
276
N
H
N
277
N
N
N
278
S
C
N
279
N
C
N
280
N
O
N
281
S
C
N
282
N
C
N
283
N
C
N
284
N
C
N
285
N
O
N
286
N
H
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
N
N
300
S
C
N
301
N
C
N
302
N
O
N
303
N
C
N
304
N
C
N
305
N
C
N
306
N
C
N
307
N
O
N
308
N
H
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
N
N
322
S
C
N
323
N
C
N
324
N
O
N
325
N
C
N
326
N
C
N
327
N
C
N
328
N
C
N
329
N
N
N
330
N
O
N
331
N
H
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
N
N
347
S
C
N
348
N
C
N
349
N
O
N
350
N
C
N
351
N
C
N
352
N
S
N
353
N
C
N
354
N
O
N
355
N
H
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
N
N
367
S
C
N
368
N
C
N
369
N
O
N
370
N
C
Y
371
N
C
Y
372
N
C
Y
373
N
C
Y
374
N
C
Y
375
N
C
Y
376
N
C
N
377
N
O
N
378
N
H
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
N
N
390
S
C
N
391
N
C
N
392
N
O
N
393
N
C
N
394
N
C
N
395
N
C
N
396
N
O
N
397
N
H
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
S
N
407
N
O
N
408
N
O
N
409
N
O
N
410
N
O
N
411
N
N
N
412
S
C
N
413
N
C
N
414
N
O
N
415
R
C
N
416
N
O
N
417
N
C
N
418
N
O
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
N
N
429
S
C
N
430
N
C
N
431
N
O
N
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
Y
436
N
N
Y
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
N
442
N
O
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
N
N
456
S
C
N
457
N
C
N
458
N
O
N
459
N
C
Y
460
N
C
Y
461
N
C
Y
462
N
C
Y
463
N
C
Y
464
N
C
Y
465
N
C
N
466
N
O
N
467
N
O
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
N
N
480
S
C
N
481
N
C
N
482
N
O
N
483
N
C
N
484
N
C
N
485
N
C
N
486
N
O
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
H
N
493
N
H
N
494
N
H
N
495
N
H
N
496
N
H
N
497
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
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
sing
N
22
N
doub
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
sing
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
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
doub
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
doub
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
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
doub
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
sing
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
doub
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
sing
N
113
N
sing
Y
114
N
doub
Y
115
N
sing
Y
116
N
sing
Y
117
N
doub
Y
118
N
doub
Y
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
doub
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
Y
129
N
doub
Y
130
N
sing
Y
131
N
sing
Y
132
N
doub
Y
133
N
doub
Y
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
doub
N
149
N
sing
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
sing
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
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
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
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
doub
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
doub
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
doub
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
sing
N
234
N
doub
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
doub
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
doub
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
Y
258
N
sing
Y
259
N
doub
Y
260
N
doub
N
261
N
sing
Y
262
N
sing
N
263
N
sing
Y
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
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
doub
N
298
N
sing
N
299
N
sing
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
sing
N
317
N
sing
N
318
N
doub
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
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
doub
N
343
N
sing
N
344
N
sing
N
345
N
sing
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
doub
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
Y
366
N
doub
Y
367
N
sing
Y
368
N
sing
N
369
N
sing
Y
370
N
doub
N
371
N
sing
Y
372
N
doub
N
373
N
sing
Y
374
N
sing
N
375
N
sing
N
376
N
sing
N
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
doub
N
385
N
sing
N
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
doub
N
396
N
doub
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
sing
N
405
N
doub
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
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
doub
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
Y
426
N
doub
Y
427
N
sing
Y
428
N
sing
N
429
N
sing
Y
430
N
doub
Y
431
N
sing
Y
432
N
sing
N
433
N
sing
Y
434
N
sing
Y
435
N
doub
N
436
N
sing
Y
437
N
doub
N
438
N
sing
Y
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
doub
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
Y
454
N
doub
Y
455
N
sing
Y
456
N
sing
N
457
N
sing
Y
458
N
doub
N
459
N
sing
Y
460
N
doub
N
461
N
sing
Y
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
sing
N
473
N
doub
N
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
US
Biochemistry
BICHAW
0033
0006-2960
47
3736
3744
10.1021/bi7023157
18311928
Crystal Structures of Highly Constrained Substrate and Hydrolysis Products Bound to HIV-1 Protease. Implications for the Catalytic Mechanism
2008
US
Biochemistry
BICHAW
0033
0006-2960
38
7978
7988
10.1021/bi990174x
10387041
Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease
1999
10.2210/pdb3bxr/pdb
pdb_00003bxr
100
1
Yale mirrors
IMAGE PLATE
1998-04-16
RIGAKU RAXIS IIC
Ni FILTER
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
0.034
1.02
1.600
50.000
1.5418
ROTATING ANODE
RIGAKU RU200
10764.701
Protease
3.4.23.16
UNP residues 491-589
Q7K, D25N, L33I, C67(ABA), C95(ABA), Q107K, D125N, L133I, C167(ABA), C195(ABA)
2
syn
polymer
96.063
SULFATE ION
4
syn
non-polymer
677.830
(9S,12S)-9-(1-methylethyl)-N-[(8S,11S)-8-[(1S)-1-methylpropyl]-7,10-dioxo-2-oxa-6,9-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-11-yl]-7,10-dioxo-2-oxa-8,11-diazabicyclo[12.2.2]octadeca-1(16),14,17-triene-12-carboxamide
1
syn
non-polymer
18.015
water
207
nat
water
Retropepsin, PR
no
yes
PQITLWKRPLVTIRIGGQLKEALLNTGADDTVIEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEI(ABA)GHKAIGTVL
VGPTPVNIIGRNLLTQIG(ABA)TLNF
PQITLWKRPLVTIRIGGQLKEALLNTGADDTVIEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEIAGHKAIGTVLVGPT
PVNIIGRNLLTQIGATLNF
A,B
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
1
2.11
41.81
VAPOR DIFFUSION, HANGING DROP
5.5
Acetate, (NH4)2SO4, pH5.5, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP
293
software
database_2
struct_conn
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Refinement description
Database references
Derived calculations
Data collection
Refinement description
Data collection
1
0
2008-03-25
1
1
2011-07-13
1
2
2017-10-25
1
3
2021-11-10
1
4
2023-11-01
1
5
2023-11-15
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
RCSB
Y
PDBJ
2008-01-14
REL
REL
0.020
0.840
0.027
0.787
0.037
1.074
0.044
1.271
0.050
1.437
0.057
0.811
0.073
1.105
0.082
0.903
0.088
0.995
0.093
0.893
SO4
SULFATE ION
DRR
(9S,12S)-9-(1-methylethyl)-N-[(8S,11S)-8-[(1S)-1-methylpropyl]-7,10-dioxo-2-oxa-6,9-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-11-yl]-7,10-dioxo-2-oxa-8,11-diazabicyclo[12.2.2]octadeca-1(16),14,17-triene-12-carboxamide
HOH
water
Chemically synthesized protein corresponding to the protease from the HIV1
sample
1CPI
PDB ENTRY 1CPI
PDB
experimental model
SO4
602
2
SO4
SO4
602
A
SO4
603
2
SO4
SO4
603
A
SO4
604
2
SO4
SO4
604
A
SO4
601
2
SO4
SO4
601
B
DRG
201
3
DRR
DRR
201
B
HOH
302
4
HOH
HOH
302
A
HOH
307
4
HOH
HOH
307
A
HOH
308
4
HOH
HOH
308
A
HOH
310
4
HOH
HOH
310
A
HOH
313
4
HOH
HOH
313
A
HOH
316
4
HOH
HOH
316
A
HOH
317
4
HOH
HOH
317
A
HOH
318
4
HOH
HOH
318
A
HOH
320
4
HOH
HOH
320
A
HOH
321
4
HOH
HOH
321
A
HOH
322
4
HOH
HOH
322
A
HOH
324
4
HOH
HOH
324
A
HOH
325
4
HOH
HOH
325
A
HOH
326
4
HOH
HOH
326
A
HOH
330
4
HOH
HOH
330
A
HOH
331
4
HOH
HOH
331
A
HOH
332
4
HOH
HOH
332
A
HOH
339
4
HOH
HOH
339
A
HOH
340
4
HOH
HOH
340
A
HOH
348
4
HOH
HOH
348
A
HOH
350
4
HOH
HOH
350
A
HOH
351
4
HOH
HOH
351
A
HOH
353
4
HOH
HOH
353
A
HOH
354
4
HOH
HOH
354
A
HOH
355
4
HOH
HOH
355
A
HOH
356
4
HOH
HOH
356
A
HOH
358
4
HOH
HOH
358
A
HOH
359
4
HOH
HOH
359
A
HOH
360
4
HOH
HOH
360
A
HOH
363
4
HOH
HOH
363
A
HOH
367
4
HOH
HOH
367
A
HOH
368
4
HOH
HOH
368
A
HOH
369
4
HOH
HOH
369
A
HOH
373
4
HOH
HOH
373
A
HOH
374
4
HOH
HOH
374
A
HOH
375
4
HOH
HOH
375
A
HOH
376
4
HOH
HOH
376
A
HOH
377
4
HOH
HOH
377
A
HOH
378
4
HOH
HOH
378
A
HOH
386
4
HOH
HOH
386
A
HOH
387
4
HOH
HOH
387
A
HOH
388
4
HOH
HOH
388
A
HOH
389
4
HOH
HOH
389
A
HOH
391
4
HOH
HOH
391
A
HOH
392
4
HOH
HOH
392
A
HOH
394
4
HOH
HOH
394
A
HOH
395
4
HOH
HOH
395
A
HOH
397
4
HOH
HOH
397
A
HOH
398
4
HOH
HOH
398
A
HOH
403
4
HOH
HOH
403
A
HOH
405
4
HOH
HOH
405
A
HOH
406
4
HOH
HOH
406
A
HOH
407
4
HOH
HOH
407
A
HOH
410
4
HOH
HOH
410
A
HOH
415
4
HOH
HOH
415
A
HOH
416
4
HOH
HOH
416
A
HOH
418
4
HOH
HOH
418
A
HOH
419
4
HOH
HOH
419
A
HOH
421
4
HOH
HOH
421
A
HOH
422
4
HOH
HOH
422
A
HOH
425
4
HOH
HOH
425
A
HOH
426
4
HOH
HOH
426
A
HOH
427
4
HOH
HOH
427
A
HOH
429
4
HOH
HOH
429
A
HOH
431
4
HOH
HOH
431
A
HOH
432
4
HOH
HOH
432
A
HOH
435
4
HOH
HOH
435
A
HOH
443
4
HOH
HOH
443
A
HOH
445
4
HOH
HOH
445
A
HOH
446
4
HOH
HOH
446
A
HOH
450
4
HOH
HOH
450
A
HOH
451
4
HOH
HOH
451
A
HOH
452
4
HOH
HOH
452
A
HOH
454
4
HOH
HOH
454
A
HOH
455
4
HOH
HOH
455
A
HOH
459
4
HOH
HOH
459
A
HOH
461
4
HOH
HOH
461
A
HOH
463
4
HOH
HOH
463
A
HOH
465
4
HOH
HOH
465
A
HOH
466
4
HOH
HOH
466
A
HOH
467
4
HOH
HOH
467
A
HOH
470
4
HOH
HOH
470
A
HOH
472
4
HOH
HOH
472
A
HOH
480
4
HOH
HOH
480
A
HOH
481
4
HOH
HOH
481
A
HOH
484
4
HOH
HOH
484
A
HOH
485
4
HOH
HOH
485
A
HOH
486
4
HOH
HOH
486
A
HOH
489
4
HOH
HOH
489
A
HOH
492
4
HOH
HOH
492
A
HOH
495
4
HOH
HOH
495
A
HOH
499
4
HOH
HOH
499
A
HOH
500
4
HOH
HOH
500
A
HOH
501
4
HOH
HOH
501
A
HOH
504
4
HOH
HOH
504
A
HOH
506
4
HOH
HOH
506
A
HOH
507
4
HOH
HOH
507
A
HOH
301
4
HOH
HOH
301
B
HOH
303
4
HOH
HOH
303
B
HOH
304
4
HOH
HOH
304
B
HOH
305
4
HOH
HOH
305
B
HOH
306
4
HOH
HOH
306
B
HOH
309
4
HOH
HOH
309
B
HOH
311
4
HOH
HOH
311
B
HOH
312
4
HOH
HOH
312
B
HOH
314
4
HOH
HOH
314
B
HOH
315
4
HOH
HOH
315
B
HOH
319
4
HOH
HOH
319
B
HOH
323
4
HOH
HOH
323
B
HOH
327
4
HOH
HOH
327
B
HOH
328
4
HOH
HOH
328
B
HOH
329
4
HOH
HOH
329
B
HOH
333
4
HOH
HOH
333
B
HOH
334
4
HOH
HOH
334
B
HOH
335
4
HOH
HOH
335
B
HOH
336
4
HOH
HOH
336
B
HOH
337
4
HOH
HOH
337
B
HOH
338
4
HOH
HOH
338
B
HOH
341
4
HOH
HOH
341
B
HOH
342
4
HOH
HOH
342
B
HOH
343
4
HOH
HOH
343
B
HOH
344
4
HOH
HOH
344
B
HOH
345
4
HOH
HOH
345
B
HOH
346
4
HOH
HOH
346
B
HOH
347
4
HOH
HOH
347
B
HOH
349
4
HOH
HOH
349
B
HOH
352
4
HOH
HOH
352
B
HOH
357
4
HOH
HOH
357
B
HOH
361
4
HOH
HOH
361
B
HOH
362
4
HOH
HOH
362
B
HOH
364
4
HOH
HOH
364
B
HOH
365
4
HOH
HOH
365
B
HOH
366
4
HOH
HOH
366
B
HOH
370
4
HOH
HOH
370
B
HOH
371
4
HOH
HOH
371
B
HOH
372
4
HOH
HOH
372
B
HOH
379
4
HOH
HOH
379
B
HOH
380
4
HOH
HOH
380
B
HOH
381
4
HOH
HOH
381
B
HOH
382
4
HOH
HOH
382
B
HOH
383
4
HOH
HOH
383
B
HOH
384
4
HOH
HOH
384
B
HOH
385
4
HOH
HOH
385
B
HOH
390
4
HOH
HOH
390
B
HOH
393
4
HOH
HOH
393
B
HOH
396
4
HOH
HOH
396
B
HOH
399
4
HOH
HOH
399
B
HOH
400
4
HOH
HOH
400
B
HOH
401
4
HOH
HOH
401
B
HOH
402
4
HOH
HOH
402
B
HOH
404
4
HOH
HOH
404
B
HOH
408
4
HOH
HOH
408
B
HOH
409
4
HOH
HOH
409
B
HOH
411
4
HOH
HOH
411
B
HOH
412
4
HOH
HOH
412
B
HOH
413
4
HOH
HOH
413
B
HOH
414
4
HOH
HOH
414
B
HOH
417
4
HOH
HOH
417
B
HOH
420
4
HOH
HOH
420
B
HOH
423
4
HOH
HOH
423
B
HOH
424
4
HOH
HOH
424
B
HOH
428
4
HOH
HOH
428
B
HOH
430
4
HOH
HOH
430
B
HOH
433
4
HOH
HOH
433
B
HOH
434
4
HOH
HOH
434
B
HOH
436
4
HOH
HOH
436
B
HOH
437
4
HOH
HOH
437
B
HOH
438
4
HOH
HOH
438
B
HOH
439
4
HOH
HOH
439
B
HOH
440
4
HOH
HOH
440
B
HOH
441
4
HOH
HOH
441
B
HOH
442
4
HOH
HOH
442
B
HOH
444
4
HOH
HOH
444
B
HOH
447
4
HOH
HOH
447
B
HOH
448
4
HOH
HOH
448
B
HOH
449
4
HOH
HOH
449
B
HOH
453
4
HOH
HOH
453
B
HOH
456
4
HOH
HOH
456
B
HOH
457
4
HOH
HOH
457
B
HOH
458
4
HOH
HOH
458
B
HOH
460
4
HOH
HOH
460
B
HOH
462
4
HOH
HOH
462
B
HOH
464
4
HOH
HOH
464
B
HOH
468
4
HOH
HOH
468
B
HOH
469
4
HOH
HOH
469
B
HOH
471
4
HOH
HOH
471
B
HOH
473
4
HOH
HOH
473
B
HOH
474
4
HOH
HOH
474
B
HOH
475
4
HOH
HOH
475
B
HOH
476
4
HOH
HOH
476
B
HOH
477
4
HOH
HOH
477
B
HOH
478
4
HOH
HOH
478
B
HOH
479
4
HOH
HOH
479
B
HOH
482
4
HOH
HOH
482
B
HOH
483
4
HOH
HOH
483
B
HOH
487
4
HOH
HOH
487
B
HOH
488
4
HOH
HOH
488
B
HOH
490
4
HOH
HOH
490
B
HOH
491
4
HOH
HOH
491
B
HOH
493
4
HOH
HOH
493
B
HOH
494
4
HOH
HOH
494
B
HOH
496
4
HOH
HOH
496
B
HOH
497
4
HOH
HOH
497
B
HOH
498
4
HOH
HOH
498
B
HOH
502
4
HOH
HOH
502
B
HOH
503
4
HOH
HOH
503
B
HOH
505
4
HOH
HOH
505
B
PRO
1
n
1
PRO
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
THR
4
n
4
THR
4
A
LEU
5
n
5
LEU
5
A
TRP
6
n
6
TRP
6
A
LYS
7
n
7
LYS
7
A
ARG
8
n
8
ARG
8
A
PRO
9
n
9
PRO
9
A
LEU
10
n
10
LEU
10
A
VAL
11
n
11
VAL
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
ARG
14
n
14
ARG
14
A
ILE
15
n
15
ILE
15
A
GLY
16
n
16
GLY
16
A
GLY
17
n
17
GLY
17
A
GLN
18
n
18
GLN
18
A
LEU
19
n
19
LEU
19
A
LYS
20
n
20
LYS
20
A
GLU
21
n
21
GLU
21
A
ALA
22
n
22
ALA
22
A
LEU
23
n
23
LEU
23
A
LEU
24
n
24
LEU
24
A
ASN
25
n
25
ASN
25
A
THR
26
n
26
THR
26
A
GLY
27
n
27
GLY
27
A
ALA
28
n
28
ALA
28
A
ASP
29
n
29
ASP
29
A
ASP
30
n
30
ASP
30
A
THR
31
n
31
THR
31
A
VAL
32
n
32
VAL
32
A
ILE
33
n
33
ILE
33
A
GLU
34
n
34
GLU
34
A
GLU
35
n
35
GLU
35
A
MET
36
n
36
MET
36
A
ASN
37
n
37
ASN
37
A
LEU
38
n
38
LEU
38
A
PRO
39
n
39
PRO
39
A
GLY
40
n
40
GLY
40
A
LYS
41
n
41
LYS
41
A
TRP
42
n
42
TRP
42
A
LYS
43
n
43
LYS
43
A
PRO
44
n
44
PRO
44
A
LYS
45
n
45
LYS
45
A
MET
46
n
46
MET
46
A
ILE
47
n
47
ILE
47
A
GLY
48
n
48
GLY
48
A
GLY
49
n
49
GLY
49
A
ILE
50
n
50
ILE
50
A
GLY
51
n
51
GLY
51
A
GLY
52
n
52
GLY
52
A
PHE
53
n
53
PHE
53
A
ILE
54
n
54
ILE
54
A
LYS
55
n
55
LYS
55
A
VAL
56
n
56
VAL
56
A
ARG
57
n
57
ARG
57
A
GLN
58
n
58
GLN
58
A
TYR
59
n
59
TYR
59
A
ASP
60
n
60
ASP
60
A
GLN
61
n
61
GLN
61
A
ILE
62
n
62
ILE
62
A
PRO
63
n
63
PRO
63
A
VAL
64
n
64
VAL
64
A
GLU
65
n
65
GLU
65
A
ILE
66
n
66
ILE
66
A
ABA
67
n
67
ABA
67
A
GLY
68
n
68
GLY
68
A
HIS
69
n
69
HIS
69
A
LYS
70
n
70
LYS
70
A
ALA
71
n
71
ALA
71
A
ILE
72
n
72
ILE
72
A
GLY
73
n
73
GLY
73
A
THR
74
n
74
THR
74
A
VAL
75
n
75
VAL
75
A
LEU
76
n
76
LEU
76
A
VAL
77
n
77
VAL
77
A
GLY
78
n
78
GLY
78
A
PRO
79
n
79
PRO
79
A
THR
80
n
80
THR
80
A
PRO
81
n
81
PRO
81
A
VAL
82
n
82
VAL
82
A
ASN
83
n
83
ASN
83
A
ILE
84
n
84
ILE
84
A
ILE
85
n
85
ILE
85
A
GLY
86
n
86
GLY
86
A
ARG
87
n
87
ARG
87
A
ASN
88
n
88
ASN
88
A
LEU
89
n
89
LEU
89
A
LEU
90
n
90
LEU
90
A
THR
91
n
91
THR
91
A
GLN
92
n
92
GLN
92
A
ILE
93
n
93
ILE
93
A
GLY
94
n
94
GLY
94
A
ABA
95
n
95
ABA
95
A
THR
96
n
96
THR
96
A
LEU
97
n
97
LEU
97
A
ASN
98
n
98
ASN
98
A
PHE
99
n
99
PHE
99
A
PRO
101
n
1
PRO
101
B
GLN
102
n
2
GLN
102
B
ILE
103
n
3
ILE
103
B
THR
104
n
4
THR
104
B
LEU
105
n
5
LEU
105
B
TRP
106
n
6
TRP
106
B
LYS
107
n
7
LYS
107
B
ARG
108
n
8
ARG
108
B
PRO
109
n
9
PRO
109
B
LEU
110
n
10
LEU
110
B
VAL
111
n
11
VAL
111
B
THR
112
n
12
THR
112
B
ILE
113
n
13
ILE
113
B
ARG
114
n
14
ARG
114
B
ILE
115
n
15
ILE
115
B
GLY
116
n
16
GLY
116
B
GLY
117
n
17
GLY
117
B
GLN
118
n
18
GLN
118
B
LEU
119
n
19
LEU
119
B
LYS
120
n
20
LYS
120
B
GLU
121
n
21
GLU
121
B
ALA
122
n
22
ALA
122
B
LEU
123
n
23
LEU
123
B
LEU
124
n
24
LEU
124
B
ASN
125
n
25
ASN
125
B
THR
126
n
26
THR
126
B
GLY
127
n
27
GLY
127
B
ALA
128
n
28
ALA
128
B
ASP
129
n
29
ASP
129
B
ASP
130
n
30
ASP
130
B
THR
131
n
31
THR
131
B
VAL
132
n
32
VAL
132
B
ILE
133
n
33
ILE
133
B
GLU
134
n
34
GLU
134
B
GLU
135
n
35
GLU
135
B
MET
136
n
36
MET
136
B
ASN
137
n
37
ASN
137
B
LEU
138
n
38
LEU
138
B
PRO
139
n
39
PRO
139
B
GLY
140
n
40
GLY
140
B
LYS
141
n
41
LYS
141
B
TRP
142
n
42
TRP
142
B
LYS
143
n
43
LYS
143
B
PRO
144
n
44
PRO
144
B
LYS
145
n
45
LYS
145
B
MET
146
n
46
MET
146
B
ILE
147
n
47
ILE
147
B
GLY
148
n
48
GLY
148
B
GLY
149
n
49
GLY
149
B
ILE
150
n
50
ILE
150
B
GLY
151
n
51
GLY
151
B
GLY
152
n
52
GLY
152
B
PHE
153
n
53
PHE
153
B
ILE
154
n
54
ILE
154
B
LYS
155
n
55
LYS
155
B
VAL
156
n
56
VAL
156
B
ARG
157
n
57
ARG
157
B
GLN
158
n
58
GLN
158
B
TYR
159
n
59
TYR
159
B
ASP
160
n
60
ASP
160
B
GLN
161
n
61
GLN
161
B
ILE
162
n
62
ILE
162
B
PRO
163
n
63
PRO
163
B
VAL
164
n
64
VAL
164
B
GLU
165
n
65
GLU
165
B
ILE
166
n
66
ILE
166
B
ABA
167
n
67
ABA
167
B
GLY
168
n
68
GLY
168
B
HIS
169
n
69
HIS
169
B
LYS
170
n
70
LYS
170
B
ALA
171
n
71
ALA
171
B
ILE
172
n
72
ILE
172
B
GLY
173
n
73
GLY
173
B
THR
174
n
74
THR
174
B
VAL
175
n
75
VAL
175
B
LEU
176
n
76
LEU
176
B
VAL
177
n
77
VAL
177
B
GLY
178
n
78
GLY
178
B
PRO
179
n
79
PRO
179
B
THR
180
n
80
THR
180
B
PRO
181
n
81
PRO
181
B
VAL
182
n
82
VAL
182
B
ASN
183
n
83
ASN
183
B
ILE
184
n
84
ILE
184
B
ILE
185
n
85
ILE
185
B
GLY
186
n
86
GLY
186
B
ARG
187
n
87
ARG
187
B
ASN
188
n
88
ASN
188
B
LEU
189
n
89
LEU
189
B
LEU
190
n
90
LEU
190
B
THR
191
n
91
THR
191
B
GLN
192
n
92
GLN
192
B
ILE
193
n
93
ILE
193
B
GLY
194
n
94
GLY
194
B
ABA
195
n
95
ABA
195
B
THR
196
n
96
THR
196
B
LEU
197
n
97
LEU
197
B
ASN
198
n
98
ASN
198
B
PHE
199
n
99
PHE
199
B
author_and_software_defined_assembly
PISA
2
dimeric
4630
-67.7
9340
A
ABA
67
ALPHA-AMINOBUTYRIC ACID
A
ABA
67
ALA
A
ABA
95
ALPHA-AMINOBUTYRIC ACID
A
ABA
95
ALA
B
ABA
167
ALPHA-AMINOBUTYRIC ACID
B
ABA
67
ALA
B
ABA
195
ALPHA-AMINOBUTYRIC ACID
B
ABA
95
ALA
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
N
ILE
3
A
N
ILE
3
B
O
LEU
197
B
O
LEU
97
B
O
THR
196
B
O
THR
96
A
N
ASN
98
A
N
ASN
98
A
N
LEU
97
A
N
LEU
97
B
O
ILE
103
B
O
ILE
3
A
N
LYS
43
A
N
LYS
43
A
O
GLN
58
A
O
GLN
58
A
N
ILE
66
A
N
ILE
66
A
O
HIS
69
A
O
HIS
69
A
O
LEU
76
A
O
LEU
76
A
N
ILE
33
A
N
ILE
33
A
N
VAL
32
A
N
VAL
32
A
O
ILE
84
A
O
ILE
84
A
O
ILE
85
A
O
ILE
85
A
N
LEU
23
A
N
LEU
23
A
O
LYS
20
A
O
LYS
20
A
N
ILE
13
A
N
ILE
13
A
N
ARG
14
A
N
ARG
14
A
O
GLU
65
A
O
GLU
65
B
N
GLY
149
B
N
GLY
49
B
O
GLY
152
B
O
GLY
52
B
N
ILE
166
B
N
ILE
66
B
O
HIS
169
B
O
HIS
69
B
O
LEU
176
B
O
LEU
76
B
N
ILE
133
B
N
ILE
33
B
N
VAL
132
B
N
VAL
32
B
O
ILE
184
B
O
ILE
84
B
O
ASN
183
B
O
ASN
83
B
N
LEU
123
B
N
LEU
23
B
O
LYS
120
B
O
LYS
20
B
N
ILE
113
B
N
ILE
13
B
N
ARG
114
B
N
ARG
14
B
O
GLU
165
B
O
GLU
65
1
A
CG
LYS
41
A
CG
LYS
41
1
Y
1
A
CD
LYS
41
A
CD
LYS
41
1
Y
1
A
CE
LYS
41
A
CE
LYS
41
1
Y
1
A
NZ
LYS
41
A
NZ
LYS
41
1
Y
1
A
CG
LYS
43
A
CG
LYS
43
1
Y
1
A
CD
LYS
43
A
CD
LYS
43
1
Y
1
A
CE
LYS
43
A
CE
LYS
43
1
Y
1
A
NZ
LYS
43
A
NZ
LYS
43
1
Y
1
B
CG
LYS
141
B
CG
LYS
41
1
Y
1
B
CD
LYS
141
B
CD
LYS
41
1
Y
1
B
CE
LYS
141
B
CE
LYS
41
1
Y
1
B
NZ
LYS
141
B
NZ
LYS
41
1
Y
1
B
CG
LYS
143
B
CG
LYS
43
1
Y
1
B
CD
LYS
143
B
CD
LYS
43
1
Y
1
B
CE
LYS
143
B
CE
LYS
43
1
Y
1
B
NZ
LYS
143
B
NZ
LYS
43
1
Y
1
B
GLU
135
-35.31
121.11
protein_rep.param
water.param
so4_dund_ch.param
subs_dund.param
14.191
0.969
0.000
0.000
-0.108
0.000
-0.861
0.204
0.179
1.600
8.0
2237
22508
22508
9.100
92.000
Random
1
THROUGHOUT
0.00
FOURIER SYNTHESIS
PDB ENTRY 1CPI
88.063
0.17
1.600
8.0
207
1829
69
0
1553
1.446
1.500
2.453
2.000
2.014
2.000
3.298
2.500
0.260
0.220
1.61
35
283
92
1.60
50
3BXR
22699
22699
0
0.034
1
22.5
3.1
91.7
0.093
1.60
1.66
5.9
1542
64.1
refinement
Axel T. Brunger
axel.brunger@yale.edu
Fortran_77
http://cns.csb.yale.edu/v1.1/
CNS
package
data extraction
PDB
sw-help@rcsb.rutgers.edu
September 10, 2007
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
3.004
data reduction
DENZO
data scaling
SCALEPACK
phasing
X-PLOR
Crystal Structures Of Highly Constrained Substrate And Hydrolysis Products Bound To HIV-1 Protease. Implications For Catalytic Mechanism
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
4
N
N
4
N
N
A
GLY
86
A
GLY
86
HELX_P
A
THR
91
A
THR
91
1
1
6
B
GLY
186
B
GLY
86
HELX_P
B
THR
191
B
THR
91
1
2
6
B
GLN
192
B
GLN
92
HELX_P
B
GLY
194
B
GLY
94
5
3
3
covale
1.329
both
A
ILE
66
A
C
ILE
66
1_555
A
ABA
67
A
N
ABA
67
1_555
covale
1.331
both
A
ABA
67
A
C
ABA
67
1_555
A
GLY
68
A
N
GLY
68
1_555
covale
1.327
both
A
GLY
94
A
C
GLY
94
1_555
A
ABA
95
A
N
ABA
95
1_555
covale
1.330
both
A
ABA
95
A
C
ABA
95
1_555
A
THR
96
A
N
THR
96
1_555
covale
1.330
both
B
ILE
166
B
C
ILE
66
1_555
B
ABA
167
B
N
ABA
67
1_555
covale
1.327
both
B
ABA
167
B
C
ABA
67
1_555
B
GLY
168
B
N
GLY
68
1_555
covale
1.328
both
B
GLY
194
B
C
GLY
94
1_555
B
ABA
195
B
N
ABA
95
1_555
covale
1.328
both
B
ABA
195
B
C
ABA
95
1_555
B
THR
196
B
N
THR
96
1_555
HYDROLASE
HIV protease, HIVPR, substrate, product, AIDS, Aspartyl protease, Capsid maturation, Core protein, Cytoplasm, DNA integration, DNA recombination, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Lipoprotein, Magnesium, Membrane, Metal-binding, Multifunctional enzyme, Myristate, Nuclease, Nucleotidyltransferase, Nucleus, Phosphoprotein, RNA-binding, RNA-directed DNA polymerase, Transferase, Viral nucleoprotein, Virion, Zinc, Zinc-finger
POL_HV1A2
UNP
1
491
P03369
PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
491
589
3BXR
1
99
P03369
A
1
1
99
491
589
3BXR
101
199
P03369
B
1
1
99
1
GLN
engineered mutation
LYS
7
3BXR
A
P03369
UNP
497
7
1
ASP
engineered mutation
ASN
25
3BXR
A
P03369
UNP
515
25
1
LEU
engineered mutation
ILE
33
3BXR
A
P03369
UNP
523
33
1
CYS
engineered mutation
ABA
67
3BXR
A
P03369
UNP
557
67
1
CYS
engineered mutation
ABA
95
3BXR
A
P03369
UNP
585
95
2
GLN
engineered mutation
LYS
107
3BXR
B
P03369
UNP
497
7
2
ASP
engineered mutation
ASN
125
3BXR
B
P03369
UNP
515
25
2
LEU
engineered mutation
ILE
133
3BXR
B
P03369
UNP
523
33
2
CYS
engineered mutation
ABA
167
3BXR
B
P03369
UNP
557
67
2
CYS
engineered mutation
ABA
195
3BXR
B
P03369
UNP
585
95
4
8
8
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
GLN
2
A
GLN
2
A
ILE
3
A
ILE
3
B
THR
196
B
THR
96
B
ASN
198
B
ASN
98
A
THR
96
A
THR
96
A
ASN
98
A
ASN
98
B
GLN
102
B
GLN
2
B
ILE
103
B
ILE
3
A
LYS
43
A
LYS
43
A
GLY
49
A
GLY
49
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
A
HIS
69
A
HIS
69
A
VAL
77
A
VAL
77
A
VAL
32
A
VAL
32
A
ILE
33
A
ILE
33
A
ILE
84
A
ILE
84
A
ILE
85
A
ILE
85
A
GLN
18
A
GLN
18
A
LEU
24
A
LEU
24
A
LEU
10
A
LEU
10
A
ILE
15
A
ILE
15
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
B
LYS
143
B
LYS
43
B
GLY
149
B
GLY
49
B
GLY
152
B
GLY
52
B
ILE
166
B
ILE
66
B
HIS
169
B
HIS
69
B
GLY
178
B
GLY
78
B
VAL
132
B
VAL
32
B
GLU
134
B
GLU
34
B
ASN
183
B
ASN
83
B
ILE
185
B
ILE
85
B
GLN
118
B
GLN
18
B
LEU
124
B
LEU
24
B
LEU
110
B
LEU
10
B
ILE
115
B
ILE
15
B
GLY
152
B
GLY
52
B
ILE
166
B
ILE
66
BINDING SITE FOR RESIDUE SO4 B 601
B
SO4
601
Software
6
BINDING SITE FOR RESIDUE SO4 A 602
A
SO4
602
Software
5
BINDING SITE FOR RESIDUE SO4 A 603
A
SO4
603
Software
11
BINDING SITE FOR RESIDUE SO4 A 604
A
SO4
604
Software
5
BINDING SITE FOR RESIDUE DRR B 201
B
DRR
201
Software
25
A
GLY
68
A
GLY
68
6
3_545
A
LYS
70
A
LYS
70
6
3_545
A
HOH
431
H
HOH
6
2_554
B
PRO
101
B
PRO
1
6
2_554
B
LYS
155
B
LYS
55
6
1_555
B
HOH
479
I
HOH
6
1_555
A
PRO
1
A
PRO
1
5
1_555
A
ARG
57
A
ARG
57
5
2_455
A
HIS
69
A
HIS
69
5
1_555
A
HOH
386
H
HOH
5
1_555
B
HOH
380
I
HOH
5
1_555
A
ARG
14
A
ARG
14
11
1_555
A
GLY
17
A
GLY
17
11
1_555
A
HOH
378
H
HOH
11
1_555
A
HOH
463
H
HOH
11
1_555
B
ARG
114
B
ARG
14
11
1_455
B
ILE
115
B
ILE
15
11
1_455
B
GLY
116
B
GLY
16
11
1_455
B
GLY
117
B
GLY
17
11
1_455
B
HOH
319
I
HOH
11
1_455
B
HOH
430
I
HOH
11
1_455
B
HOH
478
I
HOH
11
1_455
A
MET
36
A
MET
36
5
1_555
A
ASN
37
A
ASN
37
5
1_555
A
HOH
358
H
HOH
5
1_555
B
PRO
139
B
PRO
39
5
1_455
B
GLY
140
B
GLY
40
5
1_455
A
ARG
8
A
ARG
8
25
1_555
A
LEU
23
A
LEU
23
25
1_555
A
GLY
27
A
GLY
27
25
1_555
A
ALA
28
A
ALA
28
25
1_555
A
ASP
29
A
ASP
29
25
1_555
A
ILE
47
A
ILE
47
25
1_555
A
GLY
48
A
GLY
48
25
1_555
A
GLY
49
A
GLY
49
25
1_555
A
ILE
50
A
ILE
50
25
1_555
A
PRO
81
A
PRO
81
25
1_555
A
ILE
84
A
ILE
84
25
1_555
A
HOH
302
H
HOH
25
1_555
B
ARG
108
B
ARG
8
25
1_555
B
LEU
123
B
LEU
23
25
1_555
B
ASN
125
B
ASN
25
25
1_555
B
GLY
127
B
GLY
27
25
1_555
B
ALA
128
B
ALA
28
25
1_555
B
ASP
129
B
ASP
29
25
1_555
B
GLY
148
B
GLY
48
25
1_555
B
GLY
149
B
GLY
49
25
1_555
B
ILE
150
B
ILE
50
25
1_555
B
PRO
181
B
PRO
81
25
1_555
B
ILE
184
B
ILE
84
25
1_555
B
HOH
301
I
HOH
25
1_555
B
HOH
303
I
HOH
25
1_555
19
P 21 21 21