0.019643
0.000000
0.000000
0.000000
0.017166
0.000000
0.000000
0.000000
0.016354
0.00000
0.00000
0.00000
Mahalingam, B.
Louis, J.M.
Harrison, R.W.
Weber, I.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
50.908
58.255
61.148
C40 H70 N11 O8 1
833.053
N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide
Inhibitor analogues of CA-p2
peptide-like
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
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
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
N
N
9
N
C
N
10
N
N
N
11
N
N
N
12
N
N
N
13
S
C
N
14
N
C
N
15
N
O
N
16
N
C
N
17
N
C
N
18
N
C
N
19
N
N
N
20
S
C
N
21
N
C
N
22
N
C
N
23
N
C
N
24
N
C
N
25
N
C
N
26
N
N
N
27
S
C
N
28
N
C
N
29
N
O
N
30
N
C
Y
31
N
C
Y
32
N
C
Y
33
N
C
Y
34
N
C
Y
35
N
C
Y
36
N
C
N
37
N
N
N
38
S
C
N
39
N
C
N
40
N
O
N
41
N
C
N
42
N
C
N
43
N
C
N
44
N
O
N
45
N
O
N
46
N
N
N
47
S
C
N
48
N
C
N
49
N
O
N
50
N
C
N
51
N
N
N
52
S
C
N
53
N
C
N
54
N
O
N
55
N
C
N
56
N
C
N
57
N
C
N
58
N
C
N
59
N
N
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
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
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
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
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
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
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
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
N
N
131
S
C
N
132
N
C
N
133
N
O
N
134
N
C
N
135
N
O
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
N
N
144
S
C
N
145
N
C
N
146
N
O
N
147
N
C
N
148
N
C
N
149
N
C
N
150
N
N
N
151
N
C
N
152
N
N
N
153
N
N
N
154
N
O
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
N
N
171
S
C
N
172
N
C
N
173
N
O
N
174
N
C
N
175
N
C
N
176
N
O
N
177
N
N
N
178
N
O
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
N
N
188
S
C
N
189
N
C
N
190
N
O
N
191
N
C
N
192
N
C
N
193
N
O
N
194
N
O
N
195
N
O
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
N
N
204
R
C
N
205
N
C
N
206
N
O
N
207
N
C
N
208
N
S
N
209
N
O
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
N
N
218
S
C
N
219
N
C
N
220
N
O
N
221
N
C
N
222
N
C
N
223
N
C
N
224
N
O
N
225
N
N
N
226
N
O
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
H
N
236
N
H
N
237
N
N
N
238
S
C
N
239
N
C
N
240
N
O
N
241
N
C
N
242
N
C
N
243
N
C
N
244
N
O
N
245
N
O
N
246
N
O
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
N
N
257
N
C
N
258
N
C
N
259
N
O
N
260
N
O
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
N
N
267
S
C
N
268
N
C
N
269
N
O
N
270
N
C
Y
271
N
C
Y
272
N
N
Y
273
N
C
Y
274
N
C
Y
275
N
N
N
276
N
O
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
O
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
S
C
N
295
N
C
N
296
N
C
N
297
N
C
N
298
N
O
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
N
N
313
S
C
N
314
N
C
N
315
N
O
N
316
N
C
N
317
N
C
N
318
N
C
N
319
N
C
N
320
N
O
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
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
N
C
N
339
N
C
N
340
N
C
N
341
N
C
N
342
N
N
N
343
N
O
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
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
N
C
N
364
N
C
N
365
N
S
N
366
N
C
N
367
N
O
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
H
N
379
N
N
N
380
S
C
N
381
N
C
N
382
N
O
N
383
N
C
Y
384
N
C
Y
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
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
N
N
420
S
C
N
421
N
C
N
422
N
O
N
423
N
C
N
424
N
O
N
425
N
O
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
N
N
434
S
C
N
435
N
C
N
436
N
O
N
437
R
C
N
438
N
O
N
439
N
C
N
440
N
O
N
441
N
H
N
442
N
H
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
N
N
451
S
C
N
452
N
C
N
453
N
O
N
454
N
C
Y
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
N
Y
459
N
C
Y
460
N
C
Y
461
N
C
Y
462
N
C
Y
463
N
C
N
464
N
O
N
465
N
H
N
466
N
H
N
467
N
H
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
N
N
478
S
C
N
479
N
C
N
480
N
O
N
481
N
C
Y
482
N
C
Y
483
N
C
Y
484
N
C
Y
485
N
C
Y
486
N
C
Y
487
N
C
N
488
N
O
N
489
N
O
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
498
N
H
N
499
N
H
N
500
N
H
N
501
N
N
N
502
S
C
N
503
N
C
N
504
N
O
N
505
N
C
N
506
N
C
N
507
N
C
N
508
N
O
N
509
N
H
N
510
N
H
N
511
N
H
N
512
N
H
N
513
N
H
N
514
N
H
N
515
N
H
N
516
N
H
N
517
N
H
N
518
N
H
N
519
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
doub
N
21
N
sing
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
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
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
doub
N
65
N
sing
N
66
N
sing
N
67
N
sing
Y
68
N
doub
Y
69
N
sing
Y
70
N
sing
N
71
N
sing
Y
72
N
doub
N
73
N
sing
Y
74
N
doub
N
75
N
sing
Y
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
doub
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
doub
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
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
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
sing
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
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
doub
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
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
doub
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
doub
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
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
doub
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
doub
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
doub
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
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
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
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
doub
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
doub
N
256
N
sing
N
257
N
sing
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
doub
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
Y
269
N
sing
Y
270
N
doub
Y
271
N
doub
N
272
N
sing
Y
273
N
sing
N
274
N
sing
Y
275
N
sing
N
276
N
sing
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
doub
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
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
doub
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
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
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
doub
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
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
doub
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
Y
377
N
doub
Y
378
N
sing
Y
379
N
sing
N
380
N
sing
Y
381
N
doub
N
382
N
sing
Y
383
N
doub
N
384
N
sing
Y
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
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
sing
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
doub
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
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
doub
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
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
doub
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
Y
446
N
doub
Y
447
N
sing
Y
448
N
sing
N
449
N
sing
Y
450
N
doub
Y
451
N
sing
Y
452
N
sing
N
453
N
sing
Y
454
N
sing
Y
455
N
doub
N
456
N
sing
Y
457
N
doub
N
458
N
sing
Y
459
N
sing
N
460
N
sing
N
461
N
sing
N
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
doub
N
470
N
sing
N
471
N
sing
N
472
N
sing
N
473
N
sing
Y
474
N
doub
Y
475
N
sing
Y
476
N
sing
N
477
N
sing
Y
478
N
doub
N
479
N
sing
Y
480
N
doub
N
481
N
sing
Y
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
sing
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
doub
N
494
N
sing
N
495
N
sing
N
496
N
sing
N
497
N
sing
N
498
N
sing
N
499
N
sing
N
500
N
sing
N
501
N
sing
N
502
N
sing
N
503
N
sing
N
504
N
sing
US
Proteins
PSFGEY
0867
0887-3585
43
455
464
10.1002/prot.1057
11340661
Structural implications of drug-resistant mutants of HIV-1 protease: high-resolution crystal structures of the mutant protease/substrate analogue complexes.
2001
10.2210/pdb1fff/pdb
pdb_00001fff
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
90
1
CCD
1999-10-09
ADSC QUANTUM 4
SINGLE WAVELENGTH
M
x-ray
1
1.037
1.0
X12B
NSLS
1.037
SYNCHROTRON
NSLS BEAMLINE X12B
10739.691
PROTEASE RETROPEPSIN
3.4.23.16
D30N
2
man
polymer
SEQUENCE ANALOGOUS TO THE CA-p2 PROCESSING SITE IN HIV-1
833.053
N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide
1
syn
non-polymer
18.015
water
105
nat
water
E.C.3.4.23.16
no
no
PQITLWKRPLVTIKIGGQLKEALLDTGADNTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPT
PVNIIGRNLLTQIGATLNF
PQITLWKRPLVTIKIGGQLKEALLDTGADNTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPT
PVNIIGRNLLTQIGATLNF
C,D
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
Lentivirus
Escherichia
sample
11676
Human immunodeficiency virus 1
562
Escherichia coli
1
2.03
39.43
VAPOR DIFFUSION, HANGING DROP
CITRATE/PHOSPHATE BUFFER 0.05M, DTT 10MM, DMSO 10%,
SATURATED AMMONIUM SULPHATE 25-50%, PROTEIN 2-5 MG/ML, pH 5-6.5.
VAPOR DIFFUSION, HANGING DROP at 298K
298
database_2
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
entity
pdbx_entity_src_syn
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
Database references
Derived calculations
Data collection
Source and taxonomy
Structure summary
1
0
2001-06-01
1
1
2008-04-27
1
2
2011-07-13
1
3
2012-12-12
1
4
2021-11-03
1
5
2024-02-07
1
6
2024-03-13
_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
_entity.details
RCSB
Y
RCSB
2000-07-25
REL
0Q4
N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide
HOH
water
PEPTIDE INHIBITOR 0Q4 HAS A REDUCED PEPTIDE (-CH2-NH) INSTEAD
OF THE NORMAL PEPTIDE LINK (-CO-NH).
MUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO
STABILIZE THE PROTEASE FROM AUTOPROTEOLYSIS, WHILE
RETAINING ACTIVITY SIMILAR TO WILD-TYPE HIV-1 PROTEASE
Inhibitor
N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-
L-alanyl-L-norleucinamide
Peptide-like
ARG
401
2
0Q4
0Q4
401
D
HOH
3
3
HOH
HOH
100
C
HOH
4
3
HOH
HOH
101
C
HOH
5
3
HOH
HOH
102
C
HOH
8
3
HOH
HOH
103
C
HOH
9
3
HOH
HOH
104
C
HOH
11
3
HOH
HOH
105
C
HOH
19
3
HOH
HOH
106
C
HOH
20
3
HOH
HOH
107
C
HOH
22
3
HOH
HOH
108
C
HOH
25
3
HOH
HOH
109
C
HOH
26
3
HOH
HOH
110
C
HOH
28
3
HOH
HOH
111
C
HOH
33
3
HOH
HOH
112
C
HOH
35
3
HOH
HOH
113
C
HOH
39
3
HOH
HOH
114
C
HOH
41
3
HOH
HOH
115
C
HOH
42
3
HOH
HOH
116
C
HOH
44
3
HOH
HOH
117
C
HOH
46
3
HOH
HOH
118
C
HOH
47
3
HOH
HOH
119
C
HOH
49
3
HOH
HOH
120
C
HOH
51
3
HOH
HOH
121
C
HOH
52
3
HOH
HOH
122
C
HOH
53
3
HOH
HOH
123
C
HOH
60
3
HOH
HOH
124
C
HOH
63
3
HOH
HOH
125
C
HOH
68
3
HOH
HOH
126
C
HOH
70
3
HOH
HOH
127
C
HOH
74
3
HOH
HOH
128
C
HOH
80
3
HOH
HOH
129
C
HOH
82
3
HOH
HOH
130
C
HOH
85
3
HOH
HOH
131
C
HOH
91
3
HOH
HOH
132
C
HOH
109
3
HOH
HOH
133
C
HOH
119
3
HOH
HOH
134
C
HOH
125
3
HOH
HOH
135
C
HOH
126
3
HOH
HOH
136
C
HOH
129
3
HOH
HOH
137
C
HOH
130
3
HOH
HOH
138
C
HOH
134
3
HOH
HOH
139
C
HOH
139
3
HOH
HOH
140
C
HOH
145
3
HOH
HOH
141
C
HOH
148
3
HOH
HOH
142
C
HOH
152
3
HOH
HOH
143
C
HOH
171
3
HOH
HOH
144
C
HOH
175
3
HOH
HOH
145
C
HOH
177
3
HOH
HOH
146
C
HOH
178
3
HOH
HOH
147
C
HOH
180
3
HOH
HOH
148
C
HOH
6
3
HOH
HOH
6
D
HOH
7
3
HOH
HOH
7
D
HOH
64
3
HOH
HOH
64
D
HOH
77
3
HOH
HOH
77
D
HOH
96
3
HOH
HOH
96
D
HOH
1
3
HOH
HOH
200
D
HOH
2
3
HOH
HOH
201
D
HOH
10
3
HOH
HOH
202
D
HOH
12
3
HOH
HOH
203
D
HOH
14
3
HOH
HOH
204
D
HOH
15
3
HOH
HOH
205
D
HOH
16
3
HOH
HOH
206
D
HOH
18
3
HOH
HOH
207
D
HOH
21
3
HOH
HOH
208
D
HOH
23
3
HOH
HOH
209
D
HOH
24
3
HOH
HOH
210
D
HOH
27
3
HOH
HOH
211
D
HOH
29
3
HOH
HOH
212
D
HOH
31
3
HOH
HOH
213
D
HOH
34
3
HOH
HOH
214
D
HOH
37
3
HOH
HOH
215
D
HOH
40
3
HOH
HOH
216
D
HOH
43
3
HOH
HOH
217
D
HOH
45
3
HOH
HOH
218
D
HOH
48
3
HOH
HOH
219
D
HOH
50
3
HOH
HOH
220
D
HOH
54
3
HOH
HOH
221
D
HOH
57
3
HOH
HOH
222
D
HOH
59
3
HOH
HOH
223
D
HOH
61
3
HOH
HOH
224
D
HOH
62
3
HOH
HOH
225
D
HOH
65
3
HOH
HOH
226
D
HOH
66
3
HOH
HOH
227
D
HOH
71
3
HOH
HOH
228
D
HOH
73
3
HOH
HOH
229
D
HOH
76
3
HOH
HOH
230
D
HOH
78
3
HOH
HOH
231
D
HOH
79
3
HOH
HOH
232
D
HOH
86
3
HOH
HOH
233
D
HOH
87
3
HOH
HOH
234
D
HOH
92
3
HOH
HOH
235
D
HOH
97
3
HOH
HOH
236
D
HOH
101
3
HOH
HOH
237
D
HOH
108
3
HOH
HOH
238
D
HOH
123
3
HOH
HOH
239
D
HOH
132
3
HOH
HOH
240
D
HOH
136
3
HOH
HOH
241
D
HOH
151
3
HOH
HOH
242
D
HOH
153
3
HOH
HOH
243
D
HOH
154
3
HOH
HOH
244
D
HOH
155
3
HOH
HOH
245
D
HOH
161
3
HOH
HOH
246
D
HOH
176
3
HOH
HOH
247
D
HOH
179
3
HOH
HOH
248
D
HOH
110
3
HOH
HOH
249
D
HOH
168
3
HOH
HOH
250
D
PRO
1
n
1
PRO
1
C
GLN
2
n
2
GLN
2
C
ILE
3
n
3
ILE
3
C
THR
4
n
4
THR
4
C
LEU
5
n
5
LEU
5
C
TRP
6
n
6
TRP
6
C
LYS
7
n
7
LYS
7
C
ARG
8
n
8
ARG
8
C
PRO
9
n
9
PRO
9
C
LEU
10
n
10
LEU
10
C
VAL
11
n
11
VAL
11
C
THR
12
n
12
THR
12
C
ILE
13
n
13
ILE
13
C
LYS
14
n
14
LYS
14
C
ILE
15
n
15
ILE
15
C
GLY
16
n
16
GLY
16
C
GLY
17
n
17
GLY
17
C
GLN
18
n
18
GLN
18
C
LEU
19
n
19
LEU
19
C
LYS
20
n
20
LYS
20
C
GLU
21
n
21
GLU
21
C
ALA
22
n
22
ALA
22
C
LEU
23
n
23
LEU
23
C
LEU
24
n
24
LEU
24
C
ASP
25
n
25
ASP
25
C
THR
26
n
26
THR
26
C
GLY
27
n
27
GLY
27
C
ALA
28
n
28
ALA
28
C
ASP
29
n
29
ASP
29
C
ASN
30
n
30
ASN
30
C
THR
31
n
31
THR
31
C
VAL
32
n
32
VAL
32
C
ILE
33
n
33
ILE
33
C
GLU
34
n
34
GLU
34
C
GLU
35
n
35
GLU
35
C
MET
36
n
36
MET
36
C
SER
37
n
37
SER
37
C
LEU
38
n
38
LEU
38
C
PRO
39
n
39
PRO
39
C
GLY
40
n
40
GLY
40
C
ARG
41
n
41
ARG
41
C
TRP
42
n
42
TRP
42
C
LYS
43
n
43
LYS
43
C
PRO
44
n
44
PRO
44
C
LYS
45
n
45
LYS
45
C
MET
46
n
46
MET
46
C
ILE
47
n
47
ILE
47
C
GLY
48
n
48
GLY
48
C
GLY
49
n
49
GLY
49
C
ILE
50
n
50
ILE
50
C
GLY
51
n
51
GLY
51
C
GLY
52
n
52
GLY
52
C
PHE
53
n
53
PHE
53
C
ILE
54
n
54
ILE
54
C
LYS
55
n
55
LYS
55
C
VAL
56
n
56
VAL
56
C
ARG
57
n
57
ARG
57
C
GLN
58
n
58
GLN
58
C
TYR
59
n
59
TYR
59
C
ASP
60
n
60
ASP
60
C
GLN
61
n
61
GLN
61
C
ILE
62
n
62
ILE
62
C
ILE
63
n
63
ILE
63
C
ILE
64
n
64
ILE
64
C
GLU
65
n
65
GLU
65
C
ILE
66
n
66
ILE
66
C
ALA
67
n
67
ALA
67
C
GLY
68
n
68
GLY
68
C
HIS
69
n
69
HIS
69
C
LYS
70
n
70
LYS
70
C
ALA
71
n
71
ALA
71
C
ILE
72
n
72
ILE
72
C
GLY
73
n
73
GLY
73
C
THR
74
n
74
THR
74
C
VAL
75
n
75
VAL
75
C
LEU
76
n
76
LEU
76
C
VAL
77
n
77
VAL
77
C
GLY
78
n
78
GLY
78
C
PRO
79
n
79
PRO
79
C
THR
80
n
80
THR
80
C
PRO
81
n
81
PRO
81
C
VAL
82
n
82
VAL
82
C
ASN
83
n
83
ASN
83
C
ILE
84
n
84
ILE
84
C
ILE
85
n
85
ILE
85
C
GLY
86
n
86
GLY
86
C
ARG
87
n
87
ARG
87
C
ASN
88
n
88
ASN
88
C
LEU
89
n
89
LEU
89
C
LEU
90
n
90
LEU
90
C
THR
91
n
91
THR
91
C
GLN
92
n
92
GLN
92
C
ILE
93
n
93
ILE
93
C
GLY
94
n
94
GLY
94
C
ALA
95
n
95
ALA
95
C
THR
96
n
96
THR
96
C
LEU
97
n
97
LEU
97
C
ASN
98
n
98
ASN
98
C
PHE
99
n
99
PHE
99
C
PRO
101
n
1
PRO
101
D
GLN
102
n
2
GLN
102
D
ILE
103
n
3
ILE
103
D
THR
104
n
4
THR
104
D
LEU
105
n
5
LEU
105
D
TRP
106
n
6
TRP
106
D
LYS
107
n
7
LYS
107
D
ARG
108
n
8
ARG
108
D
PRO
109
n
9
PRO
109
D
LEU
110
n
10
LEU
110
D
VAL
111
n
11
VAL
111
D
THR
112
n
12
THR
112
D
ILE
113
n
13
ILE
113
D
LYS
114
n
14
LYS
114
D
ILE
115
n
15
ILE
115
D
GLY
116
n
16
GLY
116
D
GLY
117
n
17
GLY
117
D
GLN
118
n
18
GLN
118
D
LEU
119
n
19
LEU
119
D
LYS
120
n
20
LYS
120
D
GLU
121
n
21
GLU
121
D
ALA
122
n
22
ALA
122
D
LEU
123
n
23
LEU
123
D
LEU
124
n
24
LEU
124
D
ASP
125
n
25
ASP
125
D
THR
126
n
26
THR
126
D
GLY
127
n
27
GLY
127
D
ALA
128
n
28
ALA
128
D
ASP
129
n
29
ASP
129
D
ASN
130
n
30
ASN
130
D
THR
131
n
31
THR
131
D
VAL
132
n
32
VAL
132
D
ILE
133
n
33
ILE
133
D
GLU
134
n
34
GLU
134
D
GLU
135
n
35
GLU
135
D
MET
136
n
36
MET
136
D
SER
137
n
37
SER
137
D
LEU
138
n
38
LEU
138
D
PRO
139
n
39
PRO
139
D
GLY
140
n
40
GLY
140
D
ARG
141
n
41
ARG
141
D
TRP
142
n
42
TRP
142
D
LYS
143
n
43
LYS
143
D
PRO
144
n
44
PRO
144
D
LYS
145
n
45
LYS
145
D
MET
146
n
46
MET
146
D
ILE
147
n
47
ILE
147
D
GLY
148
n
48
GLY
148
D
GLY
149
n
49
GLY
149
D
ILE
150
n
50
ILE
150
D
GLY
151
n
51
GLY
151
D
GLY
152
n
52
GLY
152
D
PHE
153
n
53
PHE
153
D
ILE
154
n
54
ILE
154
D
LYS
155
n
55
LYS
155
D
VAL
156
n
56
VAL
156
D
ARG
157
n
57
ARG
157
D
GLN
158
n
58
GLN
158
D
TYR
159
n
59
TYR
159
D
ASP
160
n
60
ASP
160
D
GLN
161
n
61
GLN
161
D
ILE
162
n
62
ILE
162
D
ILE
163
n
63
ILE
163
D
ILE
164
n
64
ILE
164
D
GLU
165
n
65
GLU
165
D
ILE
166
n
66
ILE
166
D
ALA
167
n
67
ALA
167
D
GLY
168
n
68
GLY
168
D
HIS
169
n
69
HIS
169
D
LYS
170
n
70
LYS
170
D
ALA
171
n
71
ALA
171
D
ILE
172
n
72
ILE
172
D
GLY
173
n
73
GLY
173
D
THR
174
n
74
THR
174
D
VAL
175
n
75
VAL
175
D
LEU
176
n
76
LEU
176
D
VAL
177
n
77
VAL
177
D
GLY
178
n
78
GLY
178
D
PRO
179
n
79
PRO
179
D
THR
180
n
80
THR
180
D
PRO
181
n
81
PRO
181
D
VAL
182
n
82
VAL
182
D
ASN
183
n
83
ASN
183
D
ILE
184
n
84
ILE
184
D
ILE
185
n
85
ILE
185
D
GLY
186
n
86
GLY
186
D
ARG
187
n
87
ARG
187
D
ASN
188
n
88
ASN
188
D
LEU
189
n
89
LEU
189
D
LEU
190
n
90
LEU
190
D
THR
191
n
91
THR
191
D
GLN
192
n
92
GLN
192
D
ILE
193
n
93
ILE
193
D
GLY
194
n
94
GLY
194
D
ALA
195
n
95
ALA
195
D
THR
196
n
96
THR
196
D
LEU
197
n
97
LEU
197
D
ASN
198
n
98
ASN
198
D
PHE
199
n
99
PHE
199
D
author_and_software_defined_assembly
PISA
2
dimeric
5470
-28
9020
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
C
N
ILE
3
A
N
ILE
3
D
O
LEU
197
B
O
LEU
97
D
O
ASN
198
B
O
ASN
98
C
N
THR
96
A
N
THR
96
C
O
LEU
97
A
O
LEU
97
D
N
ILE
103
B
N
ILE
3
1
C
PRO
79
-69.95
55.59
0.2480000
0.2120000
1.9
8.0
865
14514
6.0
Random
1
THROUGHOUT
1.0
ENGH & HUBER
1.9
8.0
105
1676
59
0
1512
1.9
25
1FFF
0.0750000
1
0.2680000
1.90
1.99
1
98.5
phasing
AMoRE
refinement
X-PLOR
3.843
data collection
ADSC
data reduction
DENZO
data scaling
SCALEPACK
STRUCTURAL IMPLICATIONS OF DRUG RESISTANT MUTANTS OF HIV-1 PROTEASE : HIGH RESOLUTION CRYSTAL STRUCTURES OF THE MUTANT PROTEASE/SUBSTRATE ANALOG COMPLEXES.
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
The biological assembly is a dimer consisting of chains C and D
C
GLY
86
A
GLY
86
HELX_P
C
THR
91
A
THR
91
1
1
6
D
GLY
186
B
GLY
86
HELX_P
D
THR
191
B
THR
91
1
2
6
HYDROLASE/HYDROLASE INHIBITOR
HIV-1 PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
POL_HV1B5
UNP
1
69
P04587
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
69
167
1FFF
1
99
P04587
C
1
1
99
69
167
1FFF
101
199
P04587
D
1
1
99
1
GLN
engineered mutation
LYS
7
1FFF
C
P04587
UNP
75
7
1
ASP
engineered mutation
ASN
30
1FFF
C
P04587
UNP
98
30
1
LEU
engineered mutation
ILE
33
1FFF
C
P04587
UNP
101
33
1
LEU
engineered mutation
ILE
63
1FFF
C
P04587
UNP
131
63
1
CYS
engineered mutation
ALA
67
1FFF
C
P04587
UNP
135
67
1
CYS
engineered mutation
ALA
95
1FFF
C
P04587
UNP
163
95
2
GLN
engineered mutation
LYS
107
1FFF
D
P04587
UNP
75
7
2
ASP
engineered mutation
ASN
130
1FFF
D
P04587
UNP
98
30
2
LEU
engineered mutation
ILE
133
1FFF
D
P04587
UNP
101
33
2
LEU
engineered mutation
ILE
163
1FFF
D
P04587
UNP
131
63
2
CYS
engineered mutation
ALA
167
1FFF
D
P04587
UNP
135
67
2
CYS
engineered mutation
ALA
195
1FFF
D
P04587
UNP
163
95
4
anti-parallel
anti-parallel
anti-parallel
C
GLN
2
A
GLN
2
C
THR
4
A
THR
4
D
THR
196
B
THR
96
D
ASN
198
B
ASN
98
C
THR
96
A
THR
96
C
ASN
98
A
ASN
98
D
GLN
102
B
GLN
2
D
THR
104
B
THR
4
BINDING SITE FOR RESIDUE 0Q4 D 401
D
0Q4
401
Software
28
C
TRP
6
A
TRP
6
28
3_655
C
ARG
8
A
ARG
8
28
1_555
C
ASP
25
A
ASP
25
28
1_555
C
GLY
27
A
GLY
27
28
1_555
C
ALA
28
A
ALA
28
28
1_555
C
ASP
29
A
ASP
29
28
1_555
C
ASN
30
A
ASN
30
28
1_555
C
VAL
32
A
VAL
32
28
1_555
C
GLY
48
A
GLY
48
28
1_555
C
GLY
49
A
GLY
49
28
1_555
C
ILE
84
A
ILE
84
28
1_555
D
HOH
7
E
HOH
28
1_555
D
HOH
77
E
HOH
28
1_555
D
LEU
123
B
LEU
23
28
1_555
D
ASP
125
B
ASP
25
28
1_555
D
GLY
127
B
GLY
27
28
1_555
D
ALA
128
B
ALA
28
28
1_555
D
ASP
129
B
ASP
29
28
1_555
D
ASN
130
B
ASN
30
28
1_555
D
MET
146
B
MET
46
28
1_555
D
ILE
147
B
ILE
47
28
1_555
D
GLY
148
B
GLY
48
28
1_555
D
GLY
149
B
GLY
49
28
1_555
D
ILE
150
B
ILE
50
28
1_555
D
GLN
158
B
GLN
58
28
1_555
D
HOH
201
E
HOH
28
1_555
D
HOH
207
E
HOH
28
1_555
D
HOH
249
E
HOH
28
1_555
19
orthorhombic
P 21 21 21