0.017030
0.000000
0.000000
0.000000
0.011636
0.000000
0.000000
0.000000
0.021561
0.000000
0.000000
0.000000
Liu, F.
Weber, I.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
58.720
85.940
46.380
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
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
Na 1
22.990
SODIUM ION
non-polymer
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
N
N
139
S
C
N
140
N
C
N
141
N
O
N
142
N
C
Y
143
N
C
Y
144
N
N
Y
145
N
C
Y
146
N
C
Y
147
N
N
N
148
N
O
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
H
N
159
N
O
N
160
N
H
N
161
N
H
N
162
N
N
N
163
S
C
N
164
N
C
N
165
N
O
N
166
S
C
N
167
N
C
N
168
N
C
N
169
N
C
N
170
N
O
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
N
N
185
S
C
N
186
N
C
N
187
N
O
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
C
N
192
N
O
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
H
N
206
N
N
N
207
S
C
N
208
N
C
N
209
N
O
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
C
N
214
N
N
N
215
N
O
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
H
N
231
N
N
N
232
S
C
N
233
N
C
N
234
N
O
N
235
N
C
N
236
N
C
N
237
N
S
N
238
N
C
N
239
N
O
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
H
N
251
N
NA
N
252
N
N
N
253
S
C
N
254
N
C
N
255
N
O
N
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
Y
262
N
C
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
H
N
275
N
N
N
276
S
C
N
277
N
C
N
278
N
O
N
279
N
C
N
280
N
C
N
281
N
C
N
282
N
O
N
283
N
H
N
284
N
H
N
285
N
H
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
C
N
293
N
O
Y
294
N
N
Y
295
N
C
Y
296
N
C
Y
297
N
C
Y
298
N
C
Y
299
N
C
Y
300
N
C
Y
301
N
C
Y
302
N
C
Y
303
N
C
N
304
N
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
N
C
N
309
N
C
N
310
N
O
N
311
N
N
N
312
R
C
N
313
N
O
N
314
S
C
N
315
N
N
N
316
N
C
Y
317
N
C
Y
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
Y
322
N
C
N
323
N
N
N
324
N
C
N
325
S
C
N
326
N
C
N
327
N
O
N
328
N
C
N
329
S
C
N
330
N
C
N
331
N
C
N
332
N
C
N
333
N
C
N
334
S
C
N
335
N
C
N
336
N
N
N
337
N
C
N
338
N
C
N
339
N
C
N
340
N
C
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
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
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
N
N
392
S
C
N
393
N
C
N
394
N
O
N
395
N
C
N
396
N
O
N
397
N
O
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
N
N
406
S
C
N
407
N
C
N
408
N
O
N
409
R
C
N
410
N
O
N
411
N
C
N
412
N
O
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
N
N
423
S
C
N
424
N
C
N
425
N
O
N
426
N
C
Y
427
N
C
Y
428
N
C
Y
429
N
C
Y
430
N
N
Y
431
N
C
Y
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
N
436
N
O
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
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
N
N
450
S
C
N
451
N
C
N
452
N
O
N
453
N
C
Y
454
N
C
Y
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
C
Y
459
N
C
N
460
N
O
N
461
N
O
N
462
N
H
N
463
N
H
N
464
N
H
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
N
N
474
S
C
N
475
N
C
N
476
N
O
N
477
N
C
N
478
N
C
N
479
N
C
N
480
N
O
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
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
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
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
doub
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
doub
N
278
N
sing
Y
279
N
doub
Y
280
N
sing
Y
281
N
sing
Y
282
N
doub
N
283
N
sing
Y
284
N
sing
N
285
N
sing
Y
286
N
doub
Y
287
N
sing
Y
288
N
sing
N
289
N
sing
Y
290
N
doub
N
291
N
sing
Y
292
N
sing
N
293
N
sing
Y
294
N
doub
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
doub
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
doub
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
sing
N
319
N
sing
Y
320
N
doub
Y
321
N
sing
Y
322
N
sing
N
323
N
sing
Y
324
N
doub
N
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
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
doub
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
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
doub
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
sing
N
413
N
sing
N
414
N
sing
N
415
N
doub
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
Y
420
N
doub
Y
421
N
sing
Y
422
N
sing
N
423
N
sing
Y
424
N
doub
Y
425
N
sing
Y
426
N
sing
N
427
N
sing
Y
428
N
sing
Y
429
N
doub
N
430
N
sing
Y
431
N
doub
N
432
N
sing
Y
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
sing
N
442
N
sing
N
443
N
doub
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
Y
448
N
doub
Y
449
N
sing
Y
450
N
sing
N
451
N
sing
Y
452
N
doub
N
453
N
sing
Y
454
N
doub
N
455
N
sing
Y
456
N
sing
N
457
N
sing
N
458
N
sing
N
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
doub
N
468
N
sing
N
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
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/pdb3d1y/pdb
pdb_00003d1y
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
10726.649
HIV-1 Protease
3.4.23.16
I54V
2
man
polymer
22.990
SODIUM ION
1
syn
non-polymer
35.453
CHLORIDE ION
2
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
18.015
water
223
nat
water
Retropepsin, PR
no
no
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFVKVRQYDQIIIEIAGHKAIGTVLVGPT
PVNIIGRNLLTQIGATLNF
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFVKVRQYDQIIIEIAGHKAIGTVLVGPT
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
HIV-1
sample
gag-pol
11682
Human immunodeficiency virus type 1
Escherichia coli
1
2.73
54.90
VAPOR DIFFUSION, HANGING DROP
5.4
SODIUM ACETATE BUFFER, 1M NaCl, pH 5.4, 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
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
1
0
2008-05-27
1
1
2011-07-13
1
2
2013-02-27
1
3
2021-10-20
1
4
2024-02-21
_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
Mutant G48V complexed with DARUNAVIR at 1.4A resolution
Mutant I50V and inhibitor saquinavir at 1.2 A resolution
MUTANT I54M 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
NA
SODIUM ION
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
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
Inhibitor
Saquinavir
Peptide-like
NA
801
2
NA
NA
801
A
CL
802
3
CL
CL
802
A
ROC
201
4
ROC
ROC
201
A
CL
803
3
CL
CL
803
B
HOH
1001
5
HOH
HOH
1001
A
HOH
1003
5
HOH
HOH
1003
A
HOH
1004
5
HOH
HOH
1004
A
HOH
1005
5
HOH
HOH
1005
A
HOH
1007
5
HOH
HOH
1007
A
HOH
1010
5
HOH
HOH
1010
A
HOH
1012
5
HOH
HOH
1012
A
HOH
1014
5
HOH
HOH
1014
A
HOH
1020
5
HOH
HOH
1020
A
HOH
1021
5
HOH
HOH
1021
A
HOH
1023
5
HOH
HOH
1023
A
HOH
1024
5
HOH
HOH
1024
A
HOH
1025
5
HOH
HOH
1025
A
HOH
1027
5
HOH
HOH
1027
A
HOH
1031
5
HOH
HOH
1031
A
HOH
1032
5
HOH
HOH
1032
A
HOH
1034
5
HOH
HOH
1034
A
HOH
1036
5
HOH
HOH
1036
A
HOH
1039
5
HOH
HOH
1039
A
HOH
1040
5
HOH
HOH
1040
A
HOH
1042
5
HOH
HOH
1042
A
HOH
1045
5
HOH
HOH
1045
A
HOH
1046
5
HOH
HOH
1046
A
HOH
1054
5
HOH
HOH
1054
A
HOH
1055
5
HOH
HOH
1055
A
HOH
1058
5
HOH
HOH
1058
A
HOH
1061
5
HOH
HOH
1061
A
HOH
1064
5
HOH
HOH
1064
A
HOH
1065
5
HOH
HOH
1065
A
HOH
1066
5
HOH
HOH
1066
A
HOH
1067
5
HOH
HOH
1067
A
HOH
1068
5
HOH
HOH
1068
A
HOH
1073
5
HOH
HOH
1073
A
HOH
1074
5
HOH
HOH
1074
A
HOH
1077
5
HOH
HOH
1077
A
HOH
1081
5
HOH
HOH
1081
A
HOH
1082
5
HOH
HOH
1082
A
HOH
1086
5
HOH
HOH
1086
A
HOH
1088
5
HOH
HOH
1088
A
HOH
1089
5
HOH
HOH
1089
A
HOH
1090
5
HOH
HOH
1090
A
HOH
1091
5
HOH
HOH
1091
A
HOH
1092
5
HOH
HOH
1092
A
HOH
1093
5
HOH
HOH
1093
A
HOH
1094
5
HOH
HOH
1094
A
HOH
1095
5
HOH
HOH
1095
A
HOH
1096
5
HOH
HOH
1096
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
1102
5
HOH
HOH
1102
A
HOH
1106
5
HOH
HOH
1106
A
HOH
1107
5
HOH
HOH
1107
A
HOH
1108
5
HOH
HOH
1108
A
HOH
1109
5
HOH
HOH
1109
A
HOH
1110
5
HOH
HOH
1110
A
HOH
1111
5
HOH
HOH
1111
A
HOH
1114
5
HOH
HOH
1114
A
HOH
1118
5
HOH
HOH
1118
A
HOH
1122
5
HOH
HOH
1122
A
HOH
1123
5
HOH
HOH
1123
A
HOH
1125
5
HOH
HOH
1125
A
HOH
1126
5
HOH
HOH
1126
A
HOH
1127
5
HOH
HOH
1127
A
HOH
1129
5
HOH
HOH
1129
A
HOH
1130
5
HOH
HOH
1130
A
HOH
1133
5
HOH
HOH
1133
A
HOH
1134
5
HOH
HOH
1134
A
HOH
1135
5
HOH
HOH
1135
A
HOH
1138
5
HOH
HOH
1138
A
HOH
1139
5
HOH
HOH
1139
A
HOH
1141
5
HOH
HOH
1141
A
HOH
1142
5
HOH
HOH
1142
A
HOH
1144
5
HOH
HOH
1144
A
HOH
1145
5
HOH
HOH
1145
A
HOH
1146
5
HOH
HOH
1146
A
HOH
1147
5
HOH
HOH
1147
A
HOH
1149
5
HOH
HOH
1149
A
HOH
1151
5
HOH
HOH
1151
A
HOH
1155
5
HOH
HOH
1155
A
HOH
1158
5
HOH
HOH
1158
A
HOH
1161
5
HOH
HOH
1161
A
HOH
1167
5
HOH
HOH
1167
A
HOH
1168
5
HOH
HOH
1168
A
HOH
1169
5
HOH
HOH
1169
A
HOH
1170
5
HOH
HOH
1170
A
HOH
1172
5
HOH
HOH
1172
A
HOH
1173
5
HOH
HOH
1173
A
HOH
1175
5
HOH
HOH
1175
A
HOH
1176
5
HOH
HOH
1176
A
HOH
1177
5
HOH
HOH
1177
A
HOH
1183
5
HOH
HOH
1183
A
HOH
1184
5
HOH
HOH
1184
A
HOH
1186
5
HOH
HOH
1186
A
HOH
1188
5
HOH
HOH
1188
A
HOH
1190
5
HOH
HOH
1190
A
HOH
1191
5
HOH
HOH
1191
A
HOH
1192
5
HOH
HOH
1192
A
HOH
1193
5
HOH
HOH
1193
A
HOH
1195
5
HOH
HOH
1195
A
HOH
1196
5
HOH
HOH
1196
A
HOH
1197
5
HOH
HOH
1197
A
HOH
1200
5
HOH
HOH
1200
A
HOH
1201
5
HOH
HOH
1201
A
HOH
1202
5
HOH
HOH
1202
A
HOH
1204
5
HOH
HOH
1204
A
HOH
1205
5
HOH
HOH
1205
A
HOH
1210
5
HOH
HOH
1210
A
HOH
1212
5
HOH
HOH
1212
A
HOH
1214
5
HOH
HOH
1214
A
HOH
1216
5
HOH
HOH
1216
A
HOH
1219
5
HOH
HOH
1219
A
HOH
1221
5
HOH
HOH
1221
A
HOH
1002
5
HOH
HOH
1002
B
HOH
1006
5
HOH
HOH
1006
B
HOH
1008
5
HOH
HOH
1008
B
HOH
1009
5
HOH
HOH
1009
B
HOH
1011
5
HOH
HOH
1011
B
HOH
1013
5
HOH
HOH
1013
B
HOH
1015
5
HOH
HOH
1015
B
HOH
1016
5
HOH
HOH
1016
B
HOH
1017
5
HOH
HOH
1017
B
HOH
1018
5
HOH
HOH
1018
B
HOH
1019
5
HOH
HOH
1019
B
HOH
1022
5
HOH
HOH
1022
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
1033
5
HOH
HOH
1033
B
HOH
1035
5
HOH
HOH
1035
B
HOH
1037
5
HOH
HOH
1037
B
HOH
1038
5
HOH
HOH
1038
B
HOH
1041
5
HOH
HOH
1041
B
HOH
1043
5
HOH
HOH
1043
B
HOH
1044
5
HOH
HOH
1044
B
HOH
1047
5
HOH
HOH
1047
B
HOH
1048
5
HOH
HOH
1048
B
HOH
1049
5
HOH
HOH
1049
B
HOH
1050
5
HOH
HOH
1050
B
HOH
1051
5
HOH
HOH
1051
B
HOH
1052
5
HOH
HOH
1052
B
HOH
1053
5
HOH
HOH
1053
B
HOH
1056
5
HOH
HOH
1056
B
HOH
1057
5
HOH
HOH
1057
B
HOH
1059
5
HOH
HOH
1059
B
HOH
1060
5
HOH
HOH
1060
B
HOH
1062
5
HOH
HOH
1062
B
HOH
1063
5
HOH
HOH
1063
B
HOH
1069
5
HOH
HOH
1069
B
HOH
1070
5
HOH
HOH
1070
B
HOH
1071
5
HOH
HOH
1071
B
HOH
1072
5
HOH
HOH
1072
B
HOH
1075
5
HOH
HOH
1075
B
HOH
1076
5
HOH
HOH
1076
B
HOH
1078
5
HOH
HOH
1078
B
HOH
1079
5
HOH
HOH
1079
B
HOH
1080
5
HOH
HOH
1080
B
HOH
1083
5
HOH
HOH
1083
B
HOH
1084
5
HOH
HOH
1084
B
HOH
1085
5
HOH
HOH
1085
B
HOH
1087
5
HOH
HOH
1087
B
HOH
1098
5
HOH
HOH
1098
B
HOH
1103
5
HOH
HOH
1103
B
HOH
1104
5
HOH
HOH
1104
B
HOH
1105
5
HOH
HOH
1105
B
HOH
1112
5
HOH
HOH
1112
B
HOH
1113
5
HOH
HOH
1113
B
HOH
1115
5
HOH
HOH
1115
B
HOH
1116
5
HOH
HOH
1116
B
HOH
1117
5
HOH
HOH
1117
B
HOH
1119
5
HOH
HOH
1119
B
HOH
1120
5
HOH
HOH
1120
B
HOH
1121
5
HOH
HOH
1121
B
HOH
1124
5
HOH
HOH
1124
B
HOH
1128
5
HOH
HOH
1128
B
HOH
1131
5
HOH
HOH
1131
B
HOH
1132
5
HOH
HOH
1132
B
HOH
1136
5
HOH
HOH
1136
B
HOH
1137
5
HOH
HOH
1137
B
HOH
1140
5
HOH
HOH
1140
B
HOH
1143
5
HOH
HOH
1143
B
HOH
1148
5
HOH
HOH
1148
B
HOH
1150
5
HOH
HOH
1150
B
HOH
1152
5
HOH
HOH
1152
B
HOH
1153
5
HOH
HOH
1153
B
HOH
1154
5
HOH
HOH
1154
B
HOH
1156
5
HOH
HOH
1156
B
HOH
1157
5
HOH
HOH
1157
B
HOH
1159
5
HOH
HOH
1159
B
HOH
1160
5
HOH
HOH
1160
B
HOH
1162
5
HOH
HOH
1162
B
HOH
1163
5
HOH
HOH
1163
B
HOH
1164
5
HOH
HOH
1164
B
HOH
1165
5
HOH
HOH
1165
B
HOH
1166
5
HOH
HOH
1166
B
HOH
1171
5
HOH
HOH
1171
B
HOH
1174
5
HOH
HOH
1174
B
HOH
1178
5
HOH
HOH
1178
B
HOH
1179
5
HOH
HOH
1179
B
HOH
1180
5
HOH
HOH
1180
B
HOH
1181
5
HOH
HOH
1181
B
HOH
1182
5
HOH
HOH
1182
B
HOH
1185
5
HOH
HOH
1185
B
HOH
1187
5
HOH
HOH
1187
B
HOH
1189
5
HOH
HOH
1189
B
HOH
1194
5
HOH
HOH
1194
B
HOH
1198
5
HOH
HOH
1198
B
HOH
1199
5
HOH
HOH
1199
B
HOH
1203
5
HOH
HOH
1203
B
HOH
1206
5
HOH
HOH
1206
B
HOH
1207
5
HOH
HOH
1207
B
HOH
1208
5
HOH
HOH
1208
B
HOH
1209
5
HOH
HOH
1209
B
HOH
1211
5
HOH
HOH
1211
B
HOH
1213
5
HOH
HOH
1213
B
HOH
1215
5
HOH
HOH
1215
B
HOH
1217
5
HOH
HOH
1217
B
HOH
1218
5
HOH
HOH
1218
B
HOH
1220
5
HOH
HOH
1220
B
HOH
1222
5
HOH
HOH
1222
B
HOH
1223
5
HOH
HOH
1223
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
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
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
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
LYS
114
n
14
LYS
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
ASP
125
n
25
ASP
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
SER
137
n
37
SER
137
B
LEU
138
n
38
LEU
138
B
PRO
139
n
39
PRO
139
B
GLY
140
n
40
GLY
140
B
ARG
141
n
41
ARG
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
VAL
154
n
54
VAL
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
ILE
163
n
63
ILE
163
B
ILE
164
n
64
ILE
164
B
GLU
165
n
65
GLU
165
B
ILE
166
n
66
ILE
166
B
ALA
167
n
67
ALA
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
ALA
195
n
95
ALA
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
0.1375
0.1488
0.1627
0.1736
4156
5052
5.0
5.0
83460
author_and_software_defined_assembly
PISA
2
dimeric
5470
-52
9600
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
LYS
14
A
N
LYS
14
A
O
GLU
65
A
O
GLU
65
B
N
LYS
143
B
N
LYS
43
B
O
GLN
158
B
O
GLN
58
B
N
TYR
159
B
N
TYR
59
B
O
VAL
175
B
O
VAL
75
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
ILE
185
B
O
ILE
85
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
LYS
114
B
N
LYS
14
B
O
GLU
165
B
O
GLU
65
1
3.86
0.50
120.30
124.16
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
8
8
8
N
1
22.16
1.40
123.60
145.76
A
A
A
CD
NE
CZ
ARG
ARG
ARG
57
57
57
N
1
3.38
0.50
120.30
123.68
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
57
57
57
N
1
15.02
2.30
111.70
126.72
B
B
B
CD
CE
NZ
LYS
LYS
LYS
107
107
107
B
B
B
N
1
-6.02
0.90
118.30
112.28
B
B
B
CB
CG
OD2
ASP
ASP
ASP
125
125
125
N
1
-3.03
0.50
120.30
117.27
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
141
141
141
N
1
9.26
1.40
123.60
132.86
B
B
B
CD
NE
CZ
ARG
ARG
ARG
157
157
157
N
1
-4.60
0.50
120.30
115.70
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
157
157
157
N
1
5.45
0.90
118.30
123.75
B
B
B
CB
CG
OD1
ASP
ASP
ASP
160
160
160
N
1
19.50
2.50
121.70
141.20
B
B
B
C
N
CA
PRO
VAL
VAL
181
182
182
B
Y
1
3.19
0.50
120.30
123.49
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
187
187
187
N
ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
0.1736
0.15
1.05
10.00
16779
5052
101144
83460
21249
5.0
82.5
RANDOM
1
FREE R
0.0
AB INITIO
ENGH AND HUBER
17
1614.00
1782.00
1.05
10.00
223
1785
52
0
1510
0.017
0.033
0.000
0.0286
0.085
0.096
0.084
0.006
0.056
0.090
1.05
50
3D1Y
101144
83460
4
2
0.1
1
16.8
8.3
82.5
0.42
1.05
1.09
2.5
1
1.8
92.5
model building
SHELX
refinement
SHELXL-97
data collection
HKL-2000
data reduction
HKL-2000
data scaling
HKL-2000
phasing
SHELX
Crystal structure of HIV-1 mutant I54V and inhibitor SAQUINA
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
3
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
186
B
GLY
86
HELX_P
B
THR
191
B
THR
91
1
3
6
HYDROLASE/HYDROLASE INHIBITOR
DRUG RESISTANCE, HIV-1, I54V, flap mutant, AIDS, Aspartyl protease, Capsid maturation, Capsid protein, Protease, hydrolase-hydrolase inhibitor complex
POL_HV1B5
UNP
1
501
P04587
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
501
599
3D1Y
1
99
P04587
A
1
1
99
501
599
3D1Y
101
199
P04587
B
1
1
99
1
GLN
SEE REMARK 999
LYS
7
3D1Y
A
P04587
UNP
507
7
1
LEU
SEE REMARK 999
ILE
33
3D1Y
A
P04587
UNP
533
33
1
ILE
engineered mutation
VAL
54
3D1Y
A
P04587
UNP
554
54
1
LEU
SEE REMARK 999
ILE
63
3D1Y
A
P04587
UNP
563
63
1
CYS
SEE REMARK 999
ALA
67
3D1Y
A
P04587
UNP
567
67
1
CYS
SEE REMARK 999
ALA
95
3D1Y
A
P04587
UNP
595
95
2
GLN
SEE REMARK 999
LYS
107
3D1Y
B
P04587
UNP
507
7
2
LEU
SEE REMARK 999
ILE
133
3D1Y
B
P04587
UNP
533
33
2
ILE
engineered mutation
VAL
154
3D1Y
B
P04587
UNP
554
54
2
LEU
SEE REMARK 999
ILE
163
3D1Y
B
P04587
UNP
563
63
2
CYS
SEE REMARK 999
ALA
167
3D1Y
B
P04587
UNP
567
67
2
CYS
SEE REMARK 999
ALA
195
3D1Y
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
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
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
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
VAL
177
B
VAL
77
B
VAL
132
B
VAL
32
B
ILE
133
B
ILE
33
B
ILE
184
B
ILE
84
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 NA A 801
A
NA
801
Software
1
BINDING SITE FOR RESIDUE CL A 802
A
CL
802
Software
3
BINDING SITE FOR RESIDUE ROC A 201
A
ROC
201
Software
17
A
ASP
60
A
ASP
60
1
1_555
A
THR
74
A
THR
74
3
1_555
A
ASN
88
A
ASN
88
3
1_555
B
ARG
141
B
ARG
41
3
3_556
A
ASP
25
A
ASP
25
17
1_555
A
GLY
27
A
GLY
27
17
1_555
A
ALA
28
A
ALA
28
17
1_555
A
ASP
29
A
ASP
29
17
1_555
A
ASP
30
A
ASP
30
17
1_555
A
GLY
48
A
GLY
48
17
1_555
A
GLY
49
A
GLY
49
17
1_555
A
ILE
50
A
ILE
50
17
1_555
A
PRO
81
A
PRO
81
17
1_555
B
ARG
108
B
ARG
8
17
1_555
B
ASP
125
B
ASP
25
17
1_555
B
GLY
127
B
GLY
27
17
1_555
B
GLY
148
B
GLY
48
17
1_555
B
GLY
149
B
GLY
49
17
1_555
B
ILE
150
B
ILE
50
17
1_555
B
PRO
181
B
PRO
81
17
1_555
B
ILE
184
B
ILE
84
17
1_555
18
P 21 21 2