0.016241
0.009377
0.000000
0.000000
0.018753
0.000000
0.000000
0.000000
0.011889
0.00000
0.00000
0.00000
Clemente, J.C.
Moose, R.E.
Hemrajani, R.
Govindasamy, L.
Reutzel, R.
Mckenna, R.
Abandje-McKenna, M.
Goodenow, M.M.
Dunn, B.M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
61.573
61.574
84.109
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
C36 H47 N5 O4
613.789
N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
INDINAVIR
non-polymer
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
O
N
7
N
H
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
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
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
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
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
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
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
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
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
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
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
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
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
N
N
128
N
C
N
129
N
C
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
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
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
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
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
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
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
C
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
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
N
N
251
N
C
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
N
N
256
N
C
N
257
N
C
N
258
N
C
N
259
N
C
N
260
N
N
N
261
N
C
N
262
N
C
N
263
N
C
N
264
S
C
N
265
N
O
N
266
N
C
N
267
R
C
N
268
N
C
Y
269
N
C
Y
270
N
C
Y
271
N
C
Y
272
N
C
Y
273
N
C
Y
274
N
C
N
275
N
C
N
276
N
O
N
277
N
N
N
278
S
C
N
279
R
C
N
280
N
O
N
281
N
C
Y
282
N
C
Y
283
N
C
Y
284
N
C
Y
285
N
C
Y
286
N
C
Y
287
N
C
N
288
N
C
Y
289
N
C
Y
290
N
C
Y
291
N
N
Y
292
N
C
Y
293
N
C
Y
294
N
C
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
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
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
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
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
N
N
343
S
C
N
344
N
C
N
345
N
O
N
346
N
C
Y
347
N
C
Y
348
N
C
Y
349
N
C
Y
350
N
C
Y
351
N
C
Y
352
N
C
N
353
N
O
N
354
N
H
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
N
N
366
S
C
N
367
N
C
N
368
N
O
N
369
N
C
N
370
N
C
N
371
N
C
N
372
N
O
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
H
N
380
N
H
N
381
N
H
N
382
N
N
N
383
S
C
N
384
N
C
N
385
N
O
N
386
N
C
N
387
N
O
N
388
N
O
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
N
N
397
S
C
N
398
N
C
N
399
N
O
N
400
R
C
N
401
N
O
N
402
N
C
N
403
N
O
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
N
N
414
S
C
N
415
N
C
N
416
N
O
N
417
N
C
Y
418
N
C
Y
419
N
C
Y
420
N
C
Y
421
N
N
Y
422
N
C
Y
423
N
C
Y
424
N
C
Y
425
N
C
Y
426
N
C
N
427
N
O
N
428
N
H
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
H
N
439
N
H
N
440
N
N
N
441
S
C
N
442
N
C
N
443
N
O
N
444
N
C
Y
445
N
C
Y
446
N
C
Y
447
N
C
Y
448
N
C
Y
449
N
C
Y
450
N
C
N
451
N
O
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
N
N
465
S
C
N
466
N
C
N
467
N
O
N
468
N
C
N
469
N
C
N
470
N
C
N
471
N
O
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
H
N
480
N
H
N
481
N
H
N
482
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
doub
N
20
N
sing
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
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
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
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
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
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
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
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
doub
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
doub
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
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
doub
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
doub
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
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
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
doub
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
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
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
doub
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
sing
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
doub
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
sing
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
doub
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
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
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
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
Y
285
N
doub
Y
286
N
sing
Y
287
N
sing
N
288
N
sing
Y
289
N
doub
N
290
N
sing
Y
291
N
sing
N
292
N
sing
Y
293
N
doub
N
294
N
sing
N
295
N
sing
N
296
N
doub
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
sing
N
309
N
sing
Y
310
N
doub
Y
311
N
sing
Y
312
N
sing
N
313
N
sing
Y
314
N
doub
N
315
N
sing
Y
316
N
sing
N
317
N
sing
Y
318
N
doub
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
Y
323
N
sing
Y
324
N
doub
Y
325
N
doub
N
326
N
sing
Y
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
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
doub
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
Y
344
N
doub
Y
345
N
sing
Y
346
N
sing
N
347
N
sing
Y
348
N
doub
N
349
N
sing
Y
350
N
doub
N
351
N
sing
Y
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
doub
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
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
doub
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
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
doub
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
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
doub
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
Y
413
N
doub
Y
414
N
sing
Y
415
N
sing
N
416
N
sing
Y
417
N
doub
Y
418
N
sing
Y
419
N
sing
N
420
N
sing
Y
421
N
sing
Y
422
N
doub
N
423
N
sing
Y
424
N
doub
N
425
N
sing
Y
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
doub
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
Y
441
N
doub
Y
442
N
sing
Y
443
N
sing
N
444
N
sing
Y
445
N
doub
N
446
N
sing
Y
447
N
doub
N
448
N
sing
Y
449
N
sing
N
450
N
sing
N
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
doub
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
sing
N
470
N
sing
N
471
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
43
12141
12151
10.1021/bi049459m
15379553
Comparing the Accumulation of Active- and Nonactive-Site Mutations in the HIV-1 Protease.
2004
10.2210/pdb1sgu/pdb
pdb_00001sgu
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
IMAGE PLATE
RIGAKU RAXIS IV
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
10835.717
POL polyprotein
3.4.23.16
Protease
K20R, V32I, L33F, M36I, I54V, L63P, A71V, V82A, I84V, L90M
2
man
polymer
613.789
N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
1
syn
non-polymer
18.015
water
95
nat
water
Retropepsin
no
no
PQITLWQRPLVTIKIGGQLREALLDTGADDTIFEEISLPGRWKPKMIGGIGGFVKVRQYDQIPIEICGHKVIGTVLVGPT
PANVIGRNLMTQIGCTLNF
PQITLWQRPLVTIKIGGQLREALLDTGADDTIFEEISLPGRWKPKMIGGIGGFVKVRQYDQIPIEICGHKVIGTVLVGPT
PANVIGRNLMTQIGCTLNF
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
Lentivirus
Escherichia
sample
11676
Human immunodeficiency virus 1
562
Escherichia coli
1
1.98
37.33
4.50
20 mM Sodium acetate, 1.5 M ammonium Sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K, pH 4.50
software
exptl_crystal_grow
database_2
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Experimental preparation
Database references
Derived calculations
Data collection
1
0
2004-10-05
1
1
2008-04-29
1
2
2011-07-13
1
3
2017-10-11
1
4
2018-01-31
1
5
2021-10-27
1
6
2024-02-14
_exptl_crystal_grow.temp
_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
RCSB
Y
RCSB
2004-02-24
REL
REL
MK1
N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
HOH
water
MK1
2632
2
MK1
MK1
2632
B
HOH
3
3
HOH
HOH
100
A
HOH
5
3
HOH
HOH
101
A
HOH
6
3
HOH
HOH
102
A
HOH
7
3
HOH
HOH
103
A
HOH
11
3
HOH
HOH
104
A
HOH
15
3
HOH
HOH
105
A
HOH
18
3
HOH
HOH
106
A
HOH
19
3
HOH
HOH
107
A
HOH
23
3
HOH
HOH
108
A
HOH
28
3
HOH
HOH
109
A
HOH
29
3
HOH
HOH
110
A
HOH
32
3
HOH
HOH
111
A
HOH
33
3
HOH
HOH
112
A
HOH
35
3
HOH
HOH
113
A
HOH
37
3
HOH
HOH
114
A
HOH
40
3
HOH
HOH
115
A
HOH
42
3
HOH
HOH
116
A
HOH
45
3
HOH
HOH
117
A
HOH
46
3
HOH
HOH
118
A
HOH
51
3
HOH
HOH
119
A
HOH
54
3
HOH
HOH
120
A
HOH
57
3
HOH
HOH
121
A
HOH
59
3
HOH
HOH
122
A
HOH
60
3
HOH
HOH
123
A
HOH
62
3
HOH
HOH
124
A
HOH
68
3
HOH
HOH
125
A
HOH
72
3
HOH
HOH
126
A
HOH
83
3
HOH
HOH
127
A
HOH
84
3
HOH
HOH
128
A
HOH
85
3
HOH
HOH
129
A
HOH
86
3
HOH
HOH
130
A
HOH
88
3
HOH
HOH
131
A
HOH
90
3
HOH
HOH
132
A
HOH
91
3
HOH
HOH
133
A
HOH
94
3
HOH
HOH
134
A
HOH
96
3
HOH
HOH
135
A
HOH
106
3
HOH
HOH
136
A
HOH
107
3
HOH
HOH
137
A
HOH
108
3
HOH
HOH
138
A
HOH
109
3
HOH
HOH
139
A
HOH
2
3
HOH
HOH
2633
B
HOH
4
3
HOH
HOH
2634
B
HOH
8
3
HOH
HOH
2635
B
HOH
9
3
HOH
HOH
2636
B
HOH
10
3
HOH
HOH
2637
B
HOH
12
3
HOH
HOH
2638
B
HOH
13
3
HOH
HOH
2639
B
HOH
14
3
HOH
HOH
2640
B
HOH
16
3
HOH
HOH
2641
B
HOH
17
3
HOH
HOH
2642
B
HOH
20
3
HOH
HOH
2643
B
HOH
21
3
HOH
HOH
2644
B
HOH
22
3
HOH
HOH
2645
B
HOH
24
3
HOH
HOH
2646
B
HOH
26
3
HOH
HOH
2647
B
HOH
30
3
HOH
HOH
2648
B
HOH
31
3
HOH
HOH
2649
B
HOH
36
3
HOH
HOH
2650
B
HOH
38
3
HOH
HOH
2651
B
HOH
39
3
HOH
HOH
2652
B
HOH
41
3
HOH
HOH
2653
B
HOH
44
3
HOH
HOH
2654
B
HOH
48
3
HOH
HOH
2655
B
HOH
49
3
HOH
HOH
2656
B
HOH
50
3
HOH
HOH
2657
B
HOH
52
3
HOH
HOH
2658
B
HOH
53
3
HOH
HOH
2659
B
HOH
55
3
HOH
HOH
2660
B
HOH
56
3
HOH
HOH
2661
B
HOH
58
3
HOH
HOH
2662
B
HOH
63
3
HOH
HOH
2663
B
HOH
65
3
HOH
HOH
2664
B
HOH
66
3
HOH
HOH
2665
B
HOH
67
3
HOH
HOH
2666
B
HOH
69
3
HOH
HOH
2667
B
HOH
74
3
HOH
HOH
2668
B
HOH
75
3
HOH
HOH
2669
B
HOH
77
3
HOH
HOH
2670
B
HOH
78
3
HOH
HOH
2671
B
HOH
80
3
HOH
HOH
2672
B
HOH
81
3
HOH
HOH
2673
B
HOH
87
3
HOH
HOH
2674
B
HOH
92
3
HOH
HOH
2675
B
HOH
98
3
HOH
HOH
2676
B
HOH
100
3
HOH
HOH
2677
B
HOH
101
3
HOH
HOH
2678
B
HOH
102
3
HOH
HOH
2679
B
HOH
103
3
HOH
HOH
2680
B
HOH
105
3
HOH
HOH
2681
B
HOH
111
3
HOH
HOH
2682
B
HOH
112
3
HOH
HOH
2683
B
HOH
116
3
HOH
HOH
2684
B
HOH
119
3
HOH
HOH
2685
B
HOH
122
3
HOH
HOH
2686
B
HOH
123
3
HOH
HOH
2687
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
GLN
7
n
7
GLN
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
LYS
14
n
14
LYS
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
ARG
20
n
20
ARG
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
ASP
25
n
25
ASP
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
ILE
32
n
32
ILE
32
A
PHE
33
n
33
PHE
33
A
GLU
34
n
34
GLU
34
A
GLU
35
n
35
GLU
35
A
ILE
36
n
36
ILE
36
A
SER
37
n
37
SER
37
A
LEU
38
n
38
LEU
38
A
PRO
39
n
39
PRO
39
A
GLY
40
n
40
GLY
40
A
ARG
41
n
41
ARG
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
VAL
54
n
54
VAL
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
ILE
64
n
64
ILE
64
A
GLU
65
n
65
GLU
65
A
ILE
66
n
66
ILE
66
A
CYS
67
n
67
CYS
67
A
GLY
68
n
68
GLY
68
A
HIS
69
n
69
HIS
69
A
LYS
70
n
70
LYS
70
A
VAL
71
n
71
VAL
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
ALA
82
n
82
ALA
82
A
ASN
83
n
83
ASN
83
A
VAL
84
n
84
VAL
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
MET
90
n
90
MET
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
CYS
95
n
95
CYS
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
1
n
1
PRO
1
B
GLN
2
n
2
GLN
2
B
ILE
3
n
3
ILE
3
B
THR
4
n
4
THR
4
B
LEU
5
n
5
LEU
5
B
TRP
6
n
6
TRP
6
B
GLN
7
n
7
GLN
7
B
ARG
8
n
8
ARG
8
B
PRO
9
n
9
PRO
9
B
LEU
10
n
10
LEU
10
B
VAL
11
n
11
VAL
11
B
THR
12
n
12
THR
12
B
ILE
13
n
13
ILE
13
B
LYS
14
n
14
LYS
14
B
ILE
15
n
15
ILE
15
B
GLY
16
n
16
GLY
16
B
GLY
17
n
17
GLY
17
B
GLN
18
n
18
GLN
18
B
LEU
19
n
19
LEU
19
B
ARG
20
n
20
ARG
20
B
GLU
21
n
21
GLU
21
B
ALA
22
n
22
ALA
22
B
LEU
23
n
23
LEU
23
B
LEU
24
n
24
LEU
24
B
ASP
25
n
25
ASP
25
B
THR
26
n
26
THR
26
B
GLY
27
n
27
GLY
27
B
ALA
28
n
28
ALA
28
B
ASP
29
n
29
ASP
29
B
ASP
30
n
30
ASP
30
B
THR
31
n
31
THR
31
B
ILE
32
n
32
ILE
32
B
PHE
33
n
33
PHE
33
B
GLU
34
n
34
GLU
34
B
GLU
35
n
35
GLU
35
B
ILE
36
n
36
ILE
36
B
SER
37
n
37
SER
37
B
LEU
38
n
38
LEU
38
B
PRO
39
n
39
PRO
39
B
GLY
40
n
40
GLY
40
B
ARG
41
n
41
ARG
41
B
TRP
42
n
42
TRP
42
B
LYS
43
n
43
LYS
43
B
PRO
44
n
44
PRO
44
B
LYS
45
n
45
LYS
45
B
MET
46
n
46
MET
46
B
ILE
47
n
47
ILE
47
B
GLY
48
n
48
GLY
48
B
GLY
49
n
49
GLY
49
B
ILE
50
n
50
ILE
50
B
GLY
51
n
51
GLY
51
B
GLY
52
n
52
GLY
52
B
PHE
53
n
53
PHE
53
B
VAL
54
n
54
VAL
54
B
LYS
55
n
55
LYS
55
B
VAL
56
n
56
VAL
56
B
ARG
57
n
57
ARG
57
B
GLN
58
n
58
GLN
58
B
TYR
59
n
59
TYR
59
B
ASP
60
n
60
ASP
60
B
GLN
61
n
61
GLN
61
B
ILE
62
n
62
ILE
62
B
PRO
63
n
63
PRO
63
B
ILE
64
n
64
ILE
64
B
GLU
65
n
65
GLU
65
B
ILE
66
n
66
ILE
66
B
CYS
67
n
67
CYS
67
B
GLY
68
n
68
GLY
68
B
HIS
69
n
69
HIS
69
B
LYS
70
n
70
LYS
70
B
VAL
71
n
71
VAL
71
B
ILE
72
n
72
ILE
72
B
GLY
73
n
73
GLY
73
B
THR
74
n
74
THR
74
B
VAL
75
n
75
VAL
75
B
LEU
76
n
76
LEU
76
B
VAL
77
n
77
VAL
77
B
GLY
78
n
78
GLY
78
B
PRO
79
n
79
PRO
79
B
THR
80
n
80
THR
80
B
PRO
81
n
81
PRO
81
B
ALA
82
n
82
ALA
82
B
ASN
83
n
83
ASN
83
B
VAL
84
n
84
VAL
84
B
ILE
85
n
85
ILE
85
B
GLY
86
n
86
GLY
86
B
ARG
87
n
87
ARG
87
B
ASN
88
n
88
ASN
88
B
LEU
89
n
89
LEU
89
B
MET
90
n
90
MET
90
B
THR
91
n
91
THR
91
B
GLN
92
n
92
GLN
92
B
ILE
93
n
93
ILE
93
B
GLY
94
n
94
GLY
94
B
CYS
95
n
95
CYS
95
B
THR
96
n
96
THR
96
B
LEU
97
n
97
LEU
97
B
ASN
98
n
98
ASN
98
B
PHE
99
n
99
PHE
99
B
author_and_software_defined_assembly
PISA
2
dimeric
5140
-20
9480
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
97
B
O
LEU
97
B
O
THR
96
B
O
THR
96
A
N
ASN
98
A
N
ASN
98
A
N
LEU
97
A
N
LEU
97
B
O
ILE
3
B
O
ILE
3
A
N
LYS
45
A
N
LYS
45
A
O
VAL
56
A
O
VAL
56
A
N
ILE
64
A
N
ILE
64
A
O
VAL
71
A
O
VAL
71
A
O
LEU
76
A
O
LEU
76
A
N
PHE
33
A
N
PHE
33
A
N
ILE
32
A
N
ILE
32
A
O
VAL
84
A
O
VAL
84
A
O
ILE
85
A
O
ILE
85
A
N
LEU
23
A
N
LEU
23
A
O
ARG
20
A
O
ARG
20
A
N
ILE
13
A
N
ILE
13
A
N
LYS
14
A
N
LYS
14
A
O
GLU
65
A
O
GLU
65
B
N
GLY
49
B
N
GLY
49
B
O
GLY
52
B
O
GLY
52
B
N
ILE
64
B
N
ILE
64
B
O
VAL
71
B
O
VAL
71
B
O
LEU
76
B
O
LEU
76
B
N
PHE
33
B
N
PHE
33
B
N
ILE
32
B
N
ILE
32
B
O
VAL
84
B
O
VAL
84
B
O
ILE
85
B
O
ILE
85
B
N
LEU
23
B
N
LEU
23
B
O
ARG
20
B
O
ARG
20
B
N
ILE
13
B
N
ILE
13
B
N
LYS
14
B
N
LYS
14
B
O
GLU
65
B
O
GLU
65
1
A
A
OE1
O
GLU
HOH
35
119
2.03
1_555
5_554
1
A
GLU
35
32.52
76.72
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER.PARAM
WATER.TOP
INDINAVIR.PARAM
INDINAVIR.TOP
22.40
2.92000
0.82000
0.00000
2.54000
0.00000
-5.46000
0.264
0.010
0.22
0.22
1.90
19.60
675
14280
13408
5.000
94.0
RANDOM
765020.120
0.0000
1
RESTRAINED
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
ENGH & HUBER
FLAT MODEL
41.83
0.40
0.29
0.24
5.00
0.20
0.17
1.90
19.60
95
1662
45
0
1522
1.261
3.30
26.40
1.02
0.311
0.033
0.273
2.02
88
1749
6
4.80
77.70
16.40
1.900
19.600
1SGU
14298
2.000
0.056
1
9.7
96.6
1.90
1.97
0.246
80.6
refinement
CNS
1.1
data scaling
SCALEPACK
model building
O
V. 7.0
Comparing the Accumulation of Active Site and Non-active Site Mutations in the HIV-1 Protease
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
A
GLY
86
A
GLY
86
HELX_P
A
THR
91
A
THR
91
1
1
6
B
GLY
86
B
GLY
86
HELX_P
B
THR
91
B
THR
91
1
2
6
B
GLN
92
B
GLN
92
HELX_P
B
GLY
94
B
GLY
94
5
3
3
HYDROLASE
ACTIVE SITE MUTATIONS, NON-ACTIVE SITE MUTATIONS, INDINAVIR, HIV-1 PROTEASE, HYDROLASE
POL_HV1BR
UNP
1
69
P03367
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
69
167
1SGU
1
99
P03367
A
1
1
99
69
167
1SGU
1
99
P03367
B
1
1
99
1
LYS
engineered mutation
ARG
20
1SGU
A
P03367
UNP
88
20
1
VAL
engineered mutation
ILE
32
1SGU
A
P03367
UNP
100
32
1
LEU
engineered mutation
PHE
33
1SGU
A
P03367
UNP
101
33
1
MET
engineered mutation
ILE
36
1SGU
A
P03367
UNP
104
36
1
ILE
engineered mutation
VAL
54
1SGU
A
P03367
UNP
122
54
1
LEU
engineered mutation
PRO
63
1SGU
A
P03367
UNP
131
63
1
ALA
engineered mutation
VAL
71
1SGU
A
P03367
UNP
139
71
1
VAL
engineered mutation
ALA
82
1SGU
A
P03367
UNP
150
82
1
ILE
engineered mutation
VAL
84
1SGU
A
P03367
UNP
152
84
1
LEU
engineered mutation
MET
90
1SGU
A
P03367
UNP
158
90
2
LYS
engineered mutation
ARG
20
1SGU
B
P03367
UNP
88
20
2
VAL
engineered mutation
ILE
32
1SGU
B
P03367
UNP
100
32
2
LEU
engineered mutation
PHE
33
1SGU
B
P03367
UNP
101
33
2
MET
engineered mutation
ILE
36
1SGU
B
P03367
UNP
104
36
2
ILE
engineered mutation
VAL
54
1SGU
B
P03367
UNP
122
54
2
LEU
engineered mutation
PRO
63
1SGU
B
P03367
UNP
131
63
2
ALA
engineered mutation
VAL
71
1SGU
B
P03367
UNP
139
71
2
VAL
engineered mutation
ALA
82
1SGU
B
P03367
UNP
150
82
2
ILE
engineered mutation
VAL
84
1SGU
B
P03367
UNP
152
84
2
LEU
engineered mutation
MET
90
1SGU
B
P03367
UNP
158
90
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
96
B
THR
96
B
ASN
98
B
ASN
98
A
THR
96
A
THR
96
A
ASN
98
A
ASN
98
B
GLN
2
B
GLN
2
B
ILE
3
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
ILE
32
A
ILE
32
A
PHE
33
A
PHE
33
A
VAL
84
A
VAL
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
43
B
LYS
43
B
GLY
49
B
GLY
49
B
GLY
52
B
GLY
52
B
ILE
66
B
ILE
66
B
HIS
69
B
HIS
69
B
VAL
77
B
VAL
77
B
ILE
32
B
ILE
32
B
PHE
33
B
PHE
33
B
VAL
84
B
VAL
84
B
ILE
85
B
ILE
85
B
GLN
18
B
GLN
18
B
LEU
24
B
LEU
24
B
LEU
10
B
LEU
10
B
ILE
15
B
ILE
15
B
GLY
52
B
GLY
52
B
ILE
66
B
ILE
66
BINDING SITE FOR RESIDUE MK1 B 2632
B
MK1
2632
Software
21
A
ASP
25
A
ASP
25
21
1_555
A
GLY
27
A
GLY
27
21
1_555
A
ILE
47
A
ILE
47
21
1_555
A
GLY
48
A
GLY
48
21
1_555
A
GLY
49
A
GLY
49
21
1_555
A
ILE
50
A
ILE
50
21
1_555
A
PRO
81
A
PRO
81
21
1_555
A
ALA
82
A
ALA
82
21
1_555
B
ARG
8
B
ARG
8
21
1_555
B
ASP
25
B
ASP
25
21
1_555
B
GLY
27
B
GLY
27
21
1_555
B
ALA
28
B
ALA
28
21
1_555
B
ASP
29
B
ASP
29
21
1_555
B
ASP
30
B
ASP
30
21
1_555
B
ILE
47
B
ILE
47
21
1_555
B
GLY
48
B
GLY
48
21
1_555
B
ILE
50
B
ILE
50
21
1_555
B
PRO
81
B
PRO
81
21
1_555
B
HOH
2633
E
HOH
21
1_555
B
HOH
2641
E
HOH
21
1_555
B
HOH
2674
E
HOH
21
1_555
169
P 61