0.016978
0.000000
0.000000
0.000000
0.011625
0.000000
0.000000
0.000000
0.021556
0.00000
0.00000
0.00000
Liu, F.
Weber, I.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
58.900
86.020
46.390
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
Cl -1
35.453
CHLORIDE ION
non-polymer
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
C38 H50 N6 O5
670.841
(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide
Fortovase; SAQUINAVIR; RO 31-8959
peptide-like
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
CL
N
75
N
N
N
76
R
C
N
77
N
C
N
78
N
O
N
79
N
C
N
80
N
S
N
81
N
O
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
N
N
90
S
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
C
N
95
N
C
N
96
N
O
N
97
N
N
N
98
N
O
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
N
N
110
S
C
N
111
N
C
N
112
N
O
N
113
N
C
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
O
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
N
N
129
N
C
N
130
N
C
N
131
N
O
N
132
N
O
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
C
N
139
N
O
N
140
N
C
N
141
N
O
N
142
N
C
N
143
N
O
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
N
N
153
S
C
N
154
N
C
N
155
N
O
N
156
N
C
Y
157
N
C
Y
158
N
N
Y
159
N
C
Y
160
N
C
Y
161
N
N
N
162
N
O
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
O
N
174
N
H
N
175
N
H
N
176
N
N
N
177
S
C
N
178
N
C
N
179
N
O
N
180
S
C
N
181
N
C
N
182
N
C
N
183
N
C
N
184
N
O
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
N
N
199
S
C
N
200
N
C
N
201
N
O
N
202
N
C
N
203
N
C
N
204
N
C
N
205
N
C
N
206
N
O
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
H
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
N
N
221
S
C
N
222
N
C
N
223
N
O
N
224
N
C
N
225
N
C
N
226
N
C
N
227
N
C
N
228
N
N
N
229
N
O
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
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
N
N
246
S
C
N
247
N
C
N
248
N
O
N
249
N
C
N
250
N
C
N
251
N
S
N
252
N
C
N
253
N
O
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
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
N
N
266
S
C
N
267
N
C
N
268
N
O
N
269
N
C
Y
270
N
C
Y
271
N
C
Y
272
N
C
Y
273
N
C
Y
274
N
C
Y
275
N
C
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
H
N
288
N
N
N
289
S
C
N
290
N
C
N
291
N
O
N
292
N
C
N
293
N
C
N
294
N
C
N
295
N
O
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
C
N
306
N
O
Y
307
N
N
Y
308
N
C
Y
309
N
C
Y
310
N
C
Y
311
N
C
Y
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
C
N
317
N
N
N
318
S
C
N
319
N
C
N
320
N
O
N
321
N
C
N
322
N
C
N
323
N
O
N
324
N
N
N
325
R
C
N
326
N
O
N
327
S
C
N
328
N
N
N
329
N
C
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
C
N
336
N
N
N
337
N
C
N
338
S
C
N
339
N
C
N
340
N
O
N
341
N
C
N
342
S
C
N
343
N
C
N
344
N
C
N
345
N
C
N
346
N
C
N
347
S
C
N
348
N
C
N
349
N
N
N
350
N
C
N
351
N
C
N
352
N
C
N
353
N
C
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
H
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
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
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
H
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
N
N
405
S
C
N
406
N
C
N
407
N
O
N
408
N
C
N
409
N
O
N
410
N
O
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
N
N
419
S
C
N
420
N
C
N
421
N
O
N
422
R
C
N
423
N
O
N
424
N
C
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
H
N
434
N
H
N
435
N
N
N
436
S
C
N
437
N
C
N
438
N
O
N
439
N
C
Y
440
N
C
Y
441
N
C
Y
442
N
C
Y
443
N
N
Y
444
N
C
Y
445
N
C
Y
446
N
C
Y
447
N
C
Y
448
N
C
N
449
N
O
N
450
N
H
N
451
N
H
N
452
N
H
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
N
N
463
S
C
N
464
N
C
N
465
N
O
N
466
N
C
Y
467
N
C
Y
468
N
C
Y
469
N
C
Y
470
N
C
Y
471
N
C
Y
472
N
C
N
473
N
O
N
474
N
O
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
483
N
H
N
484
N
H
N
485
N
H
N
486
N
N
N
487
S
C
N
488
N
C
N
489
N
O
N
490
N
C
N
491
N
C
N
492
N
C
N
493
N
O
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
H
N
502
N
H
N
503
N
H
N
504
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
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
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
Y
153
N
sing
Y
154
N
doub
Y
155
N
doub
N
156
N
sing
Y
157
N
sing
N
158
N
sing
Y
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
doub
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
doub
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
sing
N
213
N
doub
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
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
doub
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
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
doub
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
Y
261
N
doub
Y
262
N
sing
Y
263
N
sing
N
264
N
sing
Y
265
N
doub
N
266
N
sing
Y
267
N
doub
N
268
N
sing
Y
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
doub
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
doub
N
291
N
sing
Y
292
N
doub
Y
293
N
sing
Y
294
N
sing
Y
295
N
doub
N
296
N
sing
Y
297
N
sing
N
298
N
sing
Y
299
N
doub
Y
300
N
sing
Y
301
N
sing
N
302
N
sing
Y
303
N
doub
N
304
N
sing
Y
305
N
sing
N
306
N
sing
Y
307
N
doub
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
doub
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
Y
333
N
doub
Y
334
N
sing
Y
335
N
sing
N
336
N
sing
Y
337
N
doub
N
338
N
sing
Y
339
N
doub
N
340
N
sing
Y
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
doub
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
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
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
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
sing
N
398
N
sing
N
399
N
doub
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
sing
N
426
N
sing
N
427
N
sing
N
428
N
doub
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
Y
433
N
doub
Y
434
N
sing
Y
435
N
sing
N
436
N
sing
Y
437
N
doub
Y
438
N
sing
Y
439
N
sing
N
440
N
sing
Y
441
N
sing
Y
442
N
doub
N
443
N
sing
Y
444
N
doub
N
445
N
sing
Y
446
N
sing
N
447
N
sing
N
448
N
sing
N
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
doub
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
Y
461
N
doub
Y
462
N
sing
Y
463
N
sing
N
464
N
sing
Y
465
N
doub
N
466
N
sing
Y
467
N
doub
N
468
N
sing
Y
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
sing
N
473
N
sing
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
doub
N
481
N
sing
N
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
381
102
115
10.1016/j.jmb.2008.05.062
18597780
Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir.
2008
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
365
901
10.1016/j.jmb.2006.08.007
16962136
Ultra-High Resolution Crystal Structure of HIV-1 Protease
Mutant Reveals Two Binding Sites for Clinical Inhibitor Tmc114
2006
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
354
789
10.1016/j.jmb.2005.09.095
16277992
Kinetic, Stability, and Structural Changes in High-Resolution Crystal
Structures of HIV-1 Protease with Drug-Resistant Mutations L24I, I50V, and G73S.
2005
10.2210/pdb3d1x/pdb
pdb_00003d1x
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
95.0
1
CCD
2007-06-13
MARMOSAIC 300 mm CCD
SI
SINGLE WAVELENGTH
M
x-ray
1
1.00
1.0
22-ID
APS
1.00
SYNCHROTRON
APS BEAMLINE 22-ID
10758.715
HIV-1 Protease
3.4.23.16
I54M
2
man
polymer
35.453
CHLORIDE ION
3
syn
non-polymer
670.841
(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide
1
syn
non-polymer
92.094
GLYCEROL
1
syn
non-polymer
18.015
water
250
nat
water
Retropepsin, PR
no
no
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFMKVRQYDQIIIEIAGHKAIGTVLVGPT
PVNIIGRNLLTQIGATLNF
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFMKVRQYDQIIIEIAGHKAIGTVLVGPT
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
sample
gag-pol
Human immunodeficiency virus type 1
Escherichia coli
1
2.73
54.96
VAPOR DIFFUSION, HANGING DROP
5.0
SODIUM ACETATE BUFFER, 10-15% NaCl, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
295
chem_comp
database_2
entity
pdbx_entity_nonpoly
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
Database references
Derived calculations
Structure summary
Data collection
Refinement description
1
0
2008-06-03
1
1
2011-07-13
1
2
2013-02-27
1
3
2021-10-20
1
4
2023-08-30
_chem_comp.name
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Same protein complexed with DARUNAVIR at 1.4A resolution
Mutant I50V and inhibitor saquinavir at 1.2 A resolution
Mutant I54V and inhibitor SAQUINAvir at 1.05A
Mutant I54M and inhibitor DARUNAVIR at 1.3A
MUTANT I54V AND INHIBITOR DARUNAVIA at 1.05A
RCSB
Y
RCSB
2008-05-06
REL
REL
CL
CHLORIDE ION
ROC
(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide
GOL
GLYCEROL
HOH
water
THE INHIBITOR ROC IS A HYDROXYETHYLAMINE CONTAINING
TRANSITION STATE MIMETIC.
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
1DAZ
PDB entry 1DAZ
PDB
experimental model
Inhibitor
Saquinavir
Peptide-like
CL
502
2
CL
CL
502
A
ROC
201
3
ROC
ROC
201
A
GOL
801
4
GOL
GOL
801
A
CL
501
2
CL
CL
501
B
CL
503
2
CL
CL
503
B
HOH
1001
5
HOH
HOH
1001
A
HOH
1003
5
HOH
HOH
1003
A
HOH
1005
5
HOH
HOH
1005
A
HOH
1006
5
HOH
HOH
1006
A
HOH
1007
5
HOH
HOH
1007
A
HOH
1009
5
HOH
HOH
1009
A
HOH
1010
5
HOH
HOH
1010
A
HOH
1011
5
HOH
HOH
1011
A
HOH
1012
5
HOH
HOH
1012
A
HOH
1014
5
HOH
HOH
1014
A
HOH
1017
5
HOH
HOH
1017
A
HOH
1020
5
HOH
HOH
1020
A
HOH
1025
5
HOH
HOH
1025
A
HOH
1027
5
HOH
HOH
1027
A
HOH
1032
5
HOH
HOH
1032
A
HOH
1036
5
HOH
HOH
1036
A
HOH
1037
5
HOH
HOH
1037
A
HOH
1039
5
HOH
HOH
1039
A
HOH
1043
5
HOH
HOH
1043
A
HOH
1044
5
HOH
HOH
1044
A
HOH
1045
5
HOH
HOH
1045
A
HOH
1048
5
HOH
HOH
1048
A
HOH
1049
5
HOH
HOH
1049
A
HOH
1050
5
HOH
HOH
1050
A
HOH
1054
5
HOH
HOH
1054
A
HOH
1061
5
HOH
HOH
1061
A
HOH
1062
5
HOH
HOH
1062
A
HOH
1065
5
HOH
HOH
1065
A
HOH
1067
5
HOH
HOH
1067
A
HOH
1069
5
HOH
HOH
1069
A
HOH
1071
5
HOH
HOH
1071
A
HOH
1072
5
HOH
HOH
1072
A
HOH
1074
5
HOH
HOH
1074
A
HOH
1075
5
HOH
HOH
1075
A
HOH
1076
5
HOH
HOH
1076
A
HOH
1077
5
HOH
HOH
1077
A
HOH
1080
5
HOH
HOH
1080
A
HOH
1081
5
HOH
HOH
1081
A
HOH
1084
5
HOH
HOH
1084
A
HOH
1086
5
HOH
HOH
1086
A
HOH
1087
5
HOH
HOH
1087
A
HOH
1088
5
HOH
HOH
1088
A
HOH
1089
5
HOH
HOH
1089
A
HOH
1090
5
HOH
HOH
1090
A
HOH
1094
5
HOH
HOH
1094
A
HOH
1097
5
HOH
HOH
1097
A
HOH
1099
5
HOH
HOH
1099
A
HOH
1100
5
HOH
HOH
1100
A
HOH
1101
5
HOH
HOH
1101
A
HOH
1103
5
HOH
HOH
1103
A
HOH
1105
5
HOH
HOH
1105
A
HOH
1107
5
HOH
HOH
1107
A
HOH
1108
5
HOH
HOH
1108
A
HOH
1109
5
HOH
HOH
1109
A
HOH
1114
5
HOH
HOH
1114
A
HOH
1115
5
HOH
HOH
1115
A
HOH
1118
5
HOH
HOH
1118
A
HOH
1120
5
HOH
HOH
1120
A
HOH
1123
5
HOH
HOH
1123
A
HOH
1128
5
HOH
HOH
1128
A
HOH
1129
5
HOH
HOH
1129
A
HOH
1130
5
HOH
HOH
1130
A
HOH
1131
5
HOH
HOH
1131
A
HOH
1132
5
HOH
HOH
1132
A
HOH
1133
5
HOH
HOH
1133
A
HOH
1135
5
HOH
HOH
1135
A
HOH
1136
5
HOH
HOH
1136
A
HOH
1137
5
HOH
HOH
1137
A
HOH
1140
5
HOH
HOH
1140
A
HOH
1141
5
HOH
HOH
1141
A
HOH
1142
5
HOH
HOH
1142
A
HOH
1145
5
HOH
HOH
1145
A
HOH
1146
5
HOH
HOH
1146
A
HOH
1147
5
HOH
HOH
1147
A
HOH
1152
5
HOH
HOH
1152
A
HOH
1154
5
HOH
HOH
1154
A
HOH
1160
5
HOH
HOH
1160
A
HOH
1163
5
HOH
HOH
1163
A
HOH
1164
5
HOH
HOH
1164
A
HOH
1165
5
HOH
HOH
1165
A
HOH
1166
5
HOH
HOH
1166
A
HOH
1167
5
HOH
HOH
1167
A
HOH
1169
5
HOH
HOH
1169
A
HOH
1170
5
HOH
HOH
1170
A
HOH
1173
5
HOH
HOH
1173
A
HOH
1176
5
HOH
HOH
1176
A
HOH
1179
5
HOH
HOH
1179
A
HOH
1185
5
HOH
HOH
1185
A
HOH
1189
5
HOH
HOH
1189
A
HOH
1190
5
HOH
HOH
1190
A
HOH
1191
5
HOH
HOH
1191
A
HOH
1196
5
HOH
HOH
1196
A
HOH
1197
5
HOH
HOH
1197
A
HOH
1201
5
HOH
HOH
1201
A
HOH
1203
5
HOH
HOH
1203
A
HOH
1205
5
HOH
HOH
1205
A
HOH
1208
5
HOH
HOH
1208
A
HOH
1211
5
HOH
HOH
1211
A
HOH
1213
5
HOH
HOH
1213
A
HOH
1214
5
HOH
HOH
1214
A
HOH
1215
5
HOH
HOH
1215
A
HOH
1218
5
HOH
HOH
1218
A
HOH
1221
5
HOH
HOH
1221
A
HOH
1222
5
HOH
HOH
1222
A
HOH
1224
5
HOH
HOH
1224
A
HOH
1227
5
HOH
HOH
1227
A
HOH
1228
5
HOH
HOH
1228
A
HOH
1232
5
HOH
HOH
1232
A
HOH
1233
5
HOH
HOH
1233
A
HOH
1235
5
HOH
HOH
1235
A
HOH
1240
5
HOH
HOH
1240
A
HOH
1241
5
HOH
HOH
1241
A
HOH
1244
5
HOH
HOH
1244
A
HOH
1245
5
HOH
HOH
1245
A
HOH
1248
5
HOH
HOH
1248
A
HOH
1249
5
HOH
HOH
1249
A
HOH
1250
5
HOH
HOH
1250
A
HOH
1002
5
HOH
HOH
1002
B
HOH
1004
5
HOH
HOH
1004
B
HOH
1008
5
HOH
HOH
1008
B
HOH
1013
5
HOH
HOH
1013
B
HOH
1015
5
HOH
HOH
1015
B
HOH
1016
5
HOH
HOH
1016
B
HOH
1018
5
HOH
HOH
1018
B
HOH
1019
5
HOH
HOH
1019
B
HOH
1021
5
HOH
HOH
1021
B
HOH
1022
5
HOH
HOH
1022
B
HOH
1023
5
HOH
HOH
1023
B
HOH
1024
5
HOH
HOH
1024
B
HOH
1026
5
HOH
HOH
1026
B
HOH
1028
5
HOH
HOH
1028
B
HOH
1029
5
HOH
HOH
1029
B
HOH
1030
5
HOH
HOH
1030
B
HOH
1031
5
HOH
HOH
1031
B
HOH
1033
5
HOH
HOH
1033
B
HOH
1034
5
HOH
HOH
1034
B
HOH
1035
5
HOH
HOH
1035
B
HOH
1038
5
HOH
HOH
1038
B
HOH
1040
5
HOH
HOH
1040
B
HOH
1041
5
HOH
HOH
1041
B
HOH
1042
5
HOH
HOH
1042
B
HOH
1046
5
HOH
HOH
1046
B
HOH
1047
5
HOH
HOH
1047
B
HOH
1051
5
HOH
HOH
1051
B
HOH
1052
5
HOH
HOH
1052
B
HOH
1053
5
HOH
HOH
1053
B
HOH
1055
5
HOH
HOH
1055
B
HOH
1056
5
HOH
HOH
1056
B
HOH
1057
5
HOH
HOH
1057
B
HOH
1058
5
HOH
HOH
1058
B
HOH
1059
5
HOH
HOH
1059
B
HOH
1060
5
HOH
HOH
1060
B
HOH
1063
5
HOH
HOH
1063
B
HOH
1064
5
HOH
HOH
1064
B
HOH
1066
5
HOH
HOH
1066
B
HOH
1068
5
HOH
HOH
1068
B
HOH
1070
5
HOH
HOH
1070
B
HOH
1073
5
HOH
HOH
1073
B
HOH
1078
5
HOH
HOH
1078
B
HOH
1079
5
HOH
HOH
1079
B
HOH
1082
5
HOH
HOH
1082
B
HOH
1083
5
HOH
HOH
1083
B
HOH
1085
5
HOH
HOH
1085
B
HOH
1091
5
HOH
HOH
1091
B
HOH
1092
5
HOH
HOH
1092
B
HOH
1093
5
HOH
HOH
1093
B
HOH
1095
5
HOH
HOH
1095
B
HOH
1096
5
HOH
HOH
1096
B
HOH
1098
5
HOH
HOH
1098
B
HOH
1102
5
HOH
HOH
1102
B
HOH
1104
5
HOH
HOH
1104
B
HOH
1106
5
HOH
HOH
1106
B
HOH
1110
5
HOH
HOH
1110
B
HOH
1111
5
HOH
HOH
1111
B
HOH
1112
5
HOH
HOH
1112
B
HOH
1113
5
HOH
HOH
1113
B
HOH
1116
5
HOH
HOH
1116
B
HOH
1117
5
HOH
HOH
1117
B
HOH
1119
5
HOH
HOH
1119
B
HOH
1121
5
HOH
HOH
1121
B
HOH
1122
5
HOH
HOH
1122
B
HOH
1124
5
HOH
HOH
1124
B
HOH
1125
5
HOH
HOH
1125
B
HOH
1126
5
HOH
HOH
1126
B
HOH
1127
5
HOH
HOH
1127
B
HOH
1134
5
HOH
HOH
1134
B
HOH
1138
5
HOH
HOH
1138
B
HOH
1139
5
HOH
HOH
1139
B
HOH
1143
5
HOH
HOH
1143
B
HOH
1144
5
HOH
HOH
1144
B
HOH
1148
5
HOH
HOH
1148
B
HOH
1149
5
HOH
HOH
1149
B
HOH
1150
5
HOH
HOH
1150
B
HOH
1151
5
HOH
HOH
1151
B
HOH
1153
5
HOH
HOH
1153
B
HOH
1155
5
HOH
HOH
1155
B
HOH
1156
5
HOH
HOH
1156
B
HOH
1157
5
HOH
HOH
1157
B
HOH
1158
5
HOH
HOH
1158
B
HOH
1159
5
HOH
HOH
1159
B
HOH
1161
5
HOH
HOH
1161
B
HOH
1162
5
HOH
HOH
1162
B
HOH
1168
5
HOH
HOH
1168
B
HOH
1171
5
HOH
HOH
1171
B
HOH
1172
5
HOH
HOH
1172
B
HOH
1174
5
HOH
HOH
1174
B
HOH
1175
5
HOH
HOH
1175
B
HOH
1177
5
HOH
HOH
1177
B
HOH
1178
5
HOH
HOH
1178
B
HOH
1180
5
HOH
HOH
1180
B
HOH
1181
5
HOH
HOH
1181
B
HOH
1182
5
HOH
HOH
1182
B
HOH
1183
5
HOH
HOH
1183
B
HOH
1184
5
HOH
HOH
1184
B
HOH
1186
5
HOH
HOH
1186
B
HOH
1187
5
HOH
HOH
1187
B
HOH
1188
5
HOH
HOH
1188
B
HOH
1192
5
HOH
HOH
1192
B
HOH
1193
5
HOH
HOH
1193
B
HOH
1194
5
HOH
HOH
1194
B
HOH
1195
5
HOH
HOH
1195
B
HOH
1198
5
HOH
HOH
1198
B
HOH
1199
5
HOH
HOH
1199
B
HOH
1200
5
HOH
HOH
1200
B
HOH
1202
5
HOH
HOH
1202
B
HOH
1204
5
HOH
HOH
1204
B
HOH
1206
5
HOH
HOH
1206
B
HOH
1207
5
HOH
HOH
1207
B
HOH
1209
5
HOH
HOH
1209
B
HOH
1210
5
HOH
HOH
1210
B
HOH
1212
5
HOH
HOH
1212
B
HOH
1216
5
HOH
HOH
1216
B
HOH
1217
5
HOH
HOH
1217
B
HOH
1219
5
HOH
HOH
1219
B
HOH
1220
5
HOH
HOH
1220
B
HOH
1223
5
HOH
HOH
1223
B
HOH
1225
5
HOH
HOH
1225
B
HOH
1226
5
HOH
HOH
1226
B
HOH
1229
5
HOH
HOH
1229
B
HOH
1230
5
HOH
HOH
1230
B
HOH
1231
5
HOH
HOH
1231
B
HOH
1234
5
HOH
HOH
1234
B
HOH
1236
5
HOH
HOH
1236
B
HOH
1237
5
HOH
HOH
1237
B
HOH
1238
5
HOH
HOH
1238
B
HOH
1239
5
HOH
HOH
1239
B
HOH
1242
5
HOH
HOH
1242
B
HOH
1243
5
HOH
HOH
1243
B
HOH
1246
5
HOH
HOH
1246
B
HOH
1247
5
HOH
HOH
1247
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
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
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
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
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
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
MET
54
n
54
MET
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
ILE
63
n
63
ILE
63
A
ILE
64
n
64
ILE
64
A
GLU
65
n
65
GLU
65
A
ILE
66
n
66
ILE
66
A
ALA
67
n
67
ALA
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
ALA
95
n
95
ALA
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
LYS
7
n
7
LYS
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
LYS
20
n
20
LYS
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
VAL
32
n
32
VAL
32
B
ILE
33
n
33
ILE
33
B
GLU
34
n
34
GLU
34
B
GLU
35
n
35
GLU
35
B
MET
36
n
36
MET
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
MET
54
n
54
MET
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
ILE
63
n
63
ILE
63
B
ILE
64
n
64
ILE
64
B
GLU
65
n
65
GLU
65
B
ILE
66
n
66
ILE
66
B
ALA
67
n
67
ALA
67
B
GLY
68
n
68
GLY
68
B
HIS
69
n
69
HIS
69
B
LYS
70
n
70
LYS
70
B
ALA
71
n
71
ALA
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
VAL
82
n
82
VAL
82
B
ASN
83
n
83
ASN
83
B
ILE
84
n
84
ILE
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
LEU
90
n
90
LEU
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
ALA
95
n
95
ALA
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
0.1502
0.1770
0.1827
4725
5164
5.0
5.0
95184
author_and_software_defined_assembly
PISA
2
dimeric
5680
-51
9340
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
43
A
N
LYS
43
A
O
GLN
58
A
O
GLN
58
A
N
ILE
64
A
N
ILE
64
A
O
ALA
71
A
O
ALA
71
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
LYS
14
A
N
LYS
14
A
O
GLU
65
A
O
GLU
65
B
N
LYS
43
B
N
LYS
43
B
O
GLN
58
B
O
GLN
58
B
N
ILE
66
B
N
ILE
66
B
O
HIS
69
B
O
HIS
69
B
O
LEU
76
B
O
LEU
76
B
N
ILE
33
B
N
ILE
33
B
N
VAL
32
B
N
VAL
32
B
O
ILE
84
B
O
ILE
84
B
O
ILE
85
B
O
ILE
85
B
N
LEU
23
B
N
LEU
23
B
O
LYS
20
B
O
LYS
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
HOH
1249
H
HOH
1
24.44
2.60
111.60
136.04
A
A
A
CB
CG
CD
LYS
LYS
LYS
7
7
7
N
1
14.82
1.40
123.60
138.42
A
A
A
CD
NE
CZ
ARG
ARG
ARG
41
41
41
N
1
3.71
0.50
120.30
124.01
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
41
41
41
N
1
26.49
2.00
116.20
142.69
A
A
A
CA
C
N
ILE
ILE
GLY
50
50
51
B
B
Y
1
-21.93
1.70
123.20
101.27
A
A
A
O
C
N
ILE
ILE
GLY
50
50
51
B
B
Y
1
47.19
2.10
122.30
169.49
A
A
A
C
N
CA
ILE
GLY
GLY
50
51
51
B
Y
1
20.44
1.40
123.60
144.04
A
A
A
CD
NE
CZ
ARG
ARG
ARG
57
57
57
B
B
B
N
1
7.59
1.20
123.30
130.89
A
A
A
OE1
CD
OE2
GLU
GLU
GLU
65
65
65
N
1
-12.09
1.90
110.20
98.11
A
A
A
CB
CA
C
LEU
LEU
LEU
97
97
97
A
N
1
-13.14
2.10
122.30
109.16
B
B
B
C
N
CA
ILE
GLY
GLY
50
51
51
B
B
Y
1
8.81
1.40
123.60
132.41
B
B
B
CD
NE
CZ
ARG
ARG
ARG
57
57
57
B
B
B
N
1
4.14
0.50
120.30
124.44
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
57
57
57
A
A
A
N
1
-3.48
0.50
120.30
116.82
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
57
57
57
B
B
B
N
ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
0.147
0.119
0.1547
1.05
10.00
18242
5164
103172
95184
23983
5.0
93.5
RANDOM
1
FREE R
0.0
MOLECULAR REPLACEMENT
PDB entry 1DAZ
ENGH AND HUBER
34
1590.00
1785.80
1.05
10.00
250
1820
58
0
1512
0.017
0.036
0.000
0.0313
0.094
0.108
0.046
0.006
0.038
0.094
1.05
50.0
3D1X
103172
95184
4
2
0.088
1
21.9
6.6
92.2
0.258
1.05
1.09
7.0
1
4.2
93.5
phasing
AMoRE
refinement
SHELXL-97
data collection
HKL-2000
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of HIV-1 mutant I54M and inhibitor saquinavir
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
2
N
N
2
N
N
5
N
N
5
N
N
A
GLY
86
A
GLY
86
HELX_P
A
THR
91
A
THR
91
1
1
6
A
GLN
92
A
GLN
92
HELX_P
A
GLY
94
A
GLY
94
5
2
3
B
GLY
86
B
GLY
86
HELX_P
B
THR
91
B
THR
91
1
3
6
HYDROLASE/HYDROLASE INHIBITOR
DRUG RESISTANCE, HIV-1, I54M, Flap mutant, AIDS, Aspartyl protease, Capsid maturation, Capsid protein, Hydrolase-hydrolase inhibitor complex, Viral nucleoprotein
POL_HV1B5
UNP
1
501
P04587
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
501
599
3D1X
1
99
P04587
A
1
1
99
501
599
3D1X
1
99
P04587
B
1
1
99
1
GLN
SEE REMARK 999
LYS
7
3D1X
A
P04587
UNP
507
7
1
LEU
SEE REMARK 999
ILE
33
3D1X
A
P04587
UNP
533
33
1
ILE
engineered mutation
MET
54
3D1X
A
P04587
UNP
554
54
1
LEU
SEE REMARK 999
ILE
63
3D1X
A
P04587
UNP
563
63
1
CYS
SEE REMARK 999
ALA
67
3D1X
A
P04587
UNP
567
67
1
CYS
SEE REMARK 999
ALA
95
3D1X
A
P04587
UNP
595
95
2
GLN
SEE REMARK 999
LYS
7
3D1X
B
P04587
UNP
507
7
2
LEU
SEE REMARK 999
ILE
33
3D1X
B
P04587
UNP
533
33
2
ILE
engineered mutation
MET
54
3D1X
B
P04587
UNP
554
54
2
LEU
SEE REMARK 999
ILE
63
3D1X
B
P04587
UNP
563
63
2
CYS
SEE REMARK 999
ALA
67
3D1X
B
P04587
UNP
567
67
2
CYS
SEE REMARK 999
ALA
95
3D1X
B
P04587
UNP
595
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
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
TRP
42
A
TRP
42
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
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
VAL
32
B
VAL
32
B
ILE
33
B
ILE
33
B
ILE
84
B
ILE
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 CL A 502
A
CL
502
Software
4
BINDING SITE FOR RESIDUE CL B 501
B
CL
501
Software
3
BINDING SITE FOR RESIDUE CL B 503
B
CL
503
Software
4
BINDING SITE FOR RESIDUE ROC A 201
A
ROC
201
Software
32
BINDING SITE FOR RESIDUE GOL A 801
A
GOL
801
Software
10
A
THR
74
A
THR
74
4
1_555
A
ASN
88
A
ASN
88
4
1_555
A
HOH
1131
H
HOH
4
1_555
B
ARG
41
B
ARG
41
4
3_556
A
HOH
1163
H
HOH
3
1_555
B
TRP
6
B
TRP
6
3
1_555
B
LYS
55
B
LYS
55
3
3_556
B
THR
74
B
THR
74
4
1_555
B
ASN
88
B
ASN
88
4
1_555
B
HOH
1013
I
HOH
4
1_555
B
HOH
1144
I
HOH
4
1_555
A
TRP
6
A
TRP
6
32
4_556
A
ARG
8
A
ARG
8
32
1_555
A
ASP
25
A
ASP
25
32
1_555
A
GLY
27
A
GLY
27
32
1_555
A
ALA
28
A
ALA
28
32
1_555
A
ASP
29
A
ASP
29
32
1_555
A
ASP
30
A
ASP
30
32
1_555
A
GLY
48
A
GLY
48
32
1_555
A
GLY
49
A
GLY
49
32
1_555
A
ILE
50
A
ILE
50
32
1_555
A
THR
80
A
THR
80
32
1_555
A
PRO
81
A
PRO
81
32
1_555
A
ILE
84
A
ILE
84
32
1_555
A
GOL
801
E
GOL
32
1_555
A
HOH
1005
H
HOH
32
1_555
A
HOH
1009
H
HOH
32
1_555
A
HOH
1228
H
HOH
32
1_555
B
ARG
8
B
ARG
8
32
1_555
B
ASP
25
B
ASP
25
32
1_555
B
GLY
27
B
GLY
27
32
1_555
B
ALA
28
B
ALA
28
32
1_555
B
ASP
29
B
ASP
29
32
1_555
B
ASP
30
B
ASP
30
32
1_555
B
GLY
48
B
GLY
48
32
1_555
B
GLY
49
B
GLY
49
32
1_555
B
ILE
50
B
ILE
50
32
1_555
B
PRO
81
B
PRO
81
32
1_555
B
VAL
82
B
VAL
82
32
1_555
B
ILE
84
B
ILE
84
32
1_555
B
HOH
1096
I
HOH
32
1_555
B
HOH
1117
I
HOH
32
1_555
B
HOH
1219
I
HOH
32
1_555
A
ASP
29
A
ASP
29
10
1_555
A
ASP
30
A
ASP
30
10
1_555
A
ILE
47
A
ILE
47
10
1_555
A
GLY
48
A
GLY
48
10
1_555
A
ROC
201
D
ROC
10
1_555
A
HOH
1080
H
HOH
10
1_555
A
HOH
1086
H
HOH
10
1_555
A
HOH
1129
H
HOH
10
1_555
A
HOH
1232
H
HOH
10
1_555
B
HOH
1188
I
HOH
10
1_555
18
P 21 21 2