0.015954
0.009211
0.000000
0.000000
0.018422
0.000000
0.000000
0.000000
0.012004
0.00000
0.00000
0.00000
Skalova, T.
Hasek, J.
Dohnalek, J.
Petrokova, H.
Buchtelova, E.
Soucek, M.
Majer, P.
Uhlikova, T.
Konvalinka, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
62.680
62.680
83.309
C38 H49 N5 O7
687.825
N-{(3S)-3-[(tert-butoxycarbonyl)amino]-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide
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
C2 H6 O S
78.133
BETA-MERCAPTOETHANOL
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
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
O
N
2
N
C
N
3
N
O
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
N
N
9
S
C
N
10
N
C
N
11
N
C
Y
12
N
C
Y
13
N
C
Y
14
N
C
Y
15
N
C
Y
16
N
C
Y
17
N
C
N
18
N
C
N
19
N
N
N
20
S
C
N
21
N
C
N
22
N
O
N
23
N
C
Y
24
N
C
Y
25
N
C
Y
26
N
C
Y
27
N
C
Y
28
N
C
Y
29
N
C
N
30
N
N
N
31
S
C
N
32
N
C
N
33
N
O
N
34
N
C
N
35
N
C
N
36
N
C
N
37
N
O
N
38
N
O
N
39
N
N
N
40
S
C
N
41
N
C
N
42
N
O
N
43
N
C
Y
44
N
C
Y
45
N
C
Y
46
N
C
Y
47
N
C
Y
48
N
C
Y
49
N
C
N
50
N
N
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
H
N
59
N
H
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
N
N
101
S
C
N
102
N
C
N
103
N
O
N
104
N
C
N
105
N
O
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
N
N
114
S
C
N
115
N
C
N
116
N
O
N
117
N
C
N
118
N
C
N
119
N
C
N
120
N
N
N
121
N
C
N
122
N
N
N
123
N
N
N
124
N
O
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
N
N
141
S
C
N
142
N
C
N
143
N
O
N
144
N
C
N
145
N
C
N
146
N
O
N
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
N
N
158
S
C
N
159
N
C
N
160
N
O
N
161
N
C
N
162
N
C
N
163
N
O
N
164
N
O
N
165
N
O
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
C
N
174
N
C
N
175
N
O
N
176
N
S
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
R
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
S
N
189
N
O
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
N
N
198
S
C
N
199
N
C
N
200
N
O
N
201
N
C
N
202
N
C
N
203
N
C
N
204
N
O
N
205
N
N
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
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
O
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
N
N
237
N
C
N
238
N
C
N
239
N
O
N
240
N
O
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
N
N
247
S
C
N
248
N
C
N
249
N
O
N
250
N
C
Y
251
N
C
Y
252
N
N
Y
253
N
C
Y
254
N
C
Y
255
N
N
N
256
N
O
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
H
N
266
N
H
N
267
N
O
N
268
N
H
N
269
N
H
N
270
N
N
N
271
S
C
N
272
N
C
N
273
N
O
N
274
S
C
N
275
N
C
N
276
N
C
N
277
N
C
N
278
N
O
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
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
N
N
293
S
C
N
294
N
C
N
295
N
O
N
296
N
C
N
297
N
C
N
298
N
C
N
299
N
C
N
300
N
O
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
N
N
315
S
C
N
316
N
C
N
317
N
O
N
318
N
C
N
319
N
C
N
320
N
C
N
321
N
C
N
322
N
N
N
323
N
O
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
N
N
340
S
C
N
341
N
C
N
342
N
O
N
343
N
C
N
344
N
C
N
345
N
S
N
346
N
C
N
347
N
O
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
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
Y
369
N
C
N
370
N
O
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
N
N
383
S
C
N
384
N
C
N
385
N
O
N
386
N
C
N
387
N
C
N
388
N
C
N
389
N
O
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
N
N
400
S
C
N
401
N
C
N
402
N
O
N
403
N
C
N
404
N
O
N
405
N
O
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
R
C
N
418
N
O
N
419
N
C
N
420
N
O
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
N
N
431
S
C
N
432
N
C
N
433
N
O
N
434
N
C
Y
435
N
C
Y
436
N
C
Y
437
N
C
Y
438
N
N
Y
439
N
C
Y
440
N
C
Y
441
N
C
Y
442
N
C
Y
443
N
C
N
444
N
O
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
N
N
458
S
C
N
459
N
C
N
460
N
O
N
461
N
C
Y
462
N
C
Y
463
N
C
Y
464
N
C
Y
465
N
C
Y
466
N
C
Y
467
N
C
N
468
N
O
N
469
N
O
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
N
N
482
S
C
N
483
N
C
N
484
N
O
N
485
N
C
N
486
N
C
N
487
N
C
N
488
N
O
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
H
N
493
N
H
N
494
N
H
N
495
N
H
N
496
N
H
N
497
N
H
N
498
N
H
N
499
N
H
N
1
N
doub
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
Y
27
N
doub
Y
28
N
sing
Y
29
N
sing
N
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
Y
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
Y
49
N
doub
Y
50
N
sing
Y
51
N
sing
N
52
N
sing
Y
53
N
doub
N
54
N
sing
Y
55
N
doub
N
56
N
sing
Y
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
sing
N
65
N
doub
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
doub
N
81
N
sing
N
82
N
sing
N
83
N
sing
Y
84
N
doub
Y
85
N
sing
Y
86
N
sing
N
87
N
sing
Y
88
N
doub
N
89
N
sing
Y
90
N
doub
N
91
N
sing
Y
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
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
doub
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
doub
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
doub
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
doub
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
doub
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
doub
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
doub
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
doub
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
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
doub
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
doub
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
Y
250
N
sing
Y
251
N
doub
Y
252
N
doub
N
253
N
sing
Y
254
N
sing
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
sing
N
267
N
sing
N
268
N
doub
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
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
doub
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
sing
N
309
N
sing
N
310
N
doub
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
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
doub
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
Y
358
N
doub
Y
359
N
sing
Y
360
N
sing
N
361
N
sing
Y
362
N
doub
N
363
N
sing
Y
364
N
doub
N
365
N
sing
Y
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
doub
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
doub
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
doub
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
doub
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
Y
427
N
doub
Y
428
N
sing
Y
429
N
sing
N
430
N
sing
Y
431
N
doub
Y
432
N
sing
Y
433
N
sing
N
434
N
sing
Y
435
N
sing
Y
436
N
doub
N
437
N
sing
Y
438
N
doub
N
439
N
sing
Y
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
doub
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
Y
455
N
doub
Y
456
N
sing
Y
457
N
sing
N
458
N
sing
Y
459
N
doub
N
460
N
sing
Y
461
N
doub
N
462
N
sing
Y
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
sing
N
473
N
sing
N
474
N
doub
N
475
N
sing
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
sing
US
J.Med.Chem.
JMCMAR
0151
0022-2623
46
1636
1644
10.1021/jm021079g
12699382
An Ethylenamine Inhibitor Binds Tightly to Both Wild Type and Mutant HIV-1 Proteases. Structure and Energy Study
2003
10.2210/pdb1lzq/pdb
pdb_00001lzq
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
1
CCD
2000-04-12
MARRESEARCH
Diamond (111), Sagitally focusing Ge(220) and a multilayer
SINGLE WAVELENGTH
M
x-ray
1
0.9340
1.0
ID14-1
ESRF
0.9340
SYNCHROTRON
ESRF BEAMLINE ID14-1
10819.756
PROTEASE RETROPEPSIN
3.4.23.16
A71V, V82T, I84V
2
man
polymer
687.825
N-{(3S)-3-[(tert-butoxycarbonyl)amino]-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide
1
syn
non-polymer
78.133
BETA-MERCAPTOETHANOL
1
syn
non-polymer
18.015
water
86
nat
water
HIV-1 PROTEASE
E.C.3.4.23.16
no
no
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKVIGTVLVGPT
PTNVIGRNLLTQIGCTLNF
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKVIGTVLVGPT
PTNVIGRNLLTQIGCTLNF
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
gag-pol
sample
11676
Human immunodeficiency virus 1
562
Escherichia coli
1
2.2
43.7
VAPOR DIFFUSION, HANGING DROP
4.4
NaCl, GLYCEROL, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
298.0
database_2
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Source and taxonomy
Structure summary
Version format compliance
Other
Database references
Derived calculations
Data collection
1
0
2003-04-29
1
1
2007-10-16
1
2
2011-07-13
1
3
2012-12-12
1
4
2021-10-27
1
5
2024-02-14
_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
HIV-1 protease with a similar inhibitor
HIV-1 protease with a similar inhibitor
HIV-1 protease with a similar inhibitor
RCSB
Y
RCSB
2002-06-11
REL
REL
0ZQ
N-{(3S)-3-[(tert-butoxycarbonyl)amino]-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide
BME
BETA-MERCAPTOETHANOL
HOH
water
Inhibitor
BOC-PHE-PSI[CH2CH2NH]-PHE-GLU-PHE-NH2
Peptide-like
BOC
201
2
0ZQ
0ZQ
201
A
BME
387
3
BME
BME
387
A
HOH
302
4
HOH
HOH
302
A
HOH
303
4
HOH
HOH
303
A
HOH
306
4
HOH
HOH
306
A
HOH
308
4
HOH
HOH
308
A
HOH
310
4
HOH
HOH
310
A
HOH
312
4
HOH
HOH
312
A
HOH
314
4
HOH
HOH
314
A
HOH
315
4
HOH
HOH
315
A
HOH
317
4
HOH
HOH
317
A
HOH
318
4
HOH
HOH
318
A
HOH
323
4
HOH
HOH
323
A
HOH
326
4
HOH
HOH
326
A
HOH
327
4
HOH
HOH
327
A
HOH
334
4
HOH
HOH
334
A
HOH
335
4
HOH
HOH
335
A
HOH
336
4
HOH
HOH
336
A
HOH
338
4
HOH
HOH
338
A
HOH
340
4
HOH
HOH
340
A
HOH
343
4
HOH
HOH
343
A
HOH
344
4
HOH
HOH
344
A
HOH
346
4
HOH
HOH
346
A
HOH
347
4
HOH
HOH
347
A
HOH
348
4
HOH
HOH
348
A
HOH
349
4
HOH
HOH
349
A
HOH
352
4
HOH
HOH
352
A
HOH
353
4
HOH
HOH
353
A
HOH
354
4
HOH
HOH
354
A
HOH
355
4
HOH
HOH
355
A
HOH
357
4
HOH
HOH
357
A
HOH
361
4
HOH
HOH
361
A
HOH
362
4
HOH
HOH
362
A
HOH
365
4
HOH
HOH
365
A
HOH
368
4
HOH
HOH
368
A
HOH
370
4
HOH
HOH
370
A
HOH
373
4
HOH
HOH
373
A
HOH
374
4
HOH
HOH
374
A
HOH
375
4
HOH
HOH
375
A
HOH
379
4
HOH
HOH
379
A
HOH
382
4
HOH
HOH
382
A
HOH
385
4
HOH
HOH
385
A
HOH
301
4
HOH
HOH
301
B
HOH
304
4
HOH
HOH
304
B
HOH
305
4
HOH
HOH
305
B
HOH
307
4
HOH
HOH
307
B
HOH
309
4
HOH
HOH
309
B
HOH
311
4
HOH
HOH
311
B
HOH
313
4
HOH
HOH
313
B
HOH
316
4
HOH
HOH
316
B
HOH
319
4
HOH
HOH
319
B
HOH
320
4
HOH
HOH
320
B
HOH
321
4
HOH
HOH
321
B
HOH
322
4
HOH
HOH
322
B
HOH
324
4
HOH
HOH
324
B
HOH
325
4
HOH
HOH
325
B
HOH
328
4
HOH
HOH
328
B
HOH
329
4
HOH
HOH
329
B
HOH
330
4
HOH
HOH
330
B
HOH
331
4
HOH
HOH
331
B
HOH
332
4
HOH
HOH
332
B
HOH
333
4
HOH
HOH
333
B
HOH
337
4
HOH
HOH
337
B
HOH
341
4
HOH
HOH
341
B
HOH
342
4
HOH
HOH
342
B
HOH
345
4
HOH
HOH
345
B
HOH
350
4
HOH
HOH
350
B
HOH
351
4
HOH
HOH
351
B
HOH
356
4
HOH
HOH
356
B
HOH
358
4
HOH
HOH
358
B
HOH
359
4
HOH
HOH
359
B
HOH
360
4
HOH
HOH
360
B
HOH
363
4
HOH
HOH
363
B
HOH
364
4
HOH
HOH
364
B
HOH
366
4
HOH
HOH
366
B
HOH
367
4
HOH
HOH
367
B
HOH
369
4
HOH
HOH
369
B
HOH
371
4
HOH
HOH
371
B
HOH
372
4
HOH
HOH
372
B
HOH
376
4
HOH
HOH
376
B
HOH
377
4
HOH
HOH
377
B
HOH
378
4
HOH
HOH
378
B
HOH
380
4
HOH
HOH
380
B
HOH
381
4
HOH
HOH
381
B
HOH
383
4
HOH
HOH
383
B
HOH
384
4
HOH
HOH
384
B
HOH
386
4
HOH
HOH
386
B
HOH
389
4
HOH
HOH
389
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
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
LEU
33
n
33
LEU
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
ILE
54
n
54
ILE
54
A
LYS
55
n
55
LYS
55
A
VAL
56
n
56
VAL
56
A
ARG
57
n
57
ARG
57
A
GLN
58
n
58
GLN
58
A
TYR
59
n
59
TYR
59
A
ASP
60
n
60
ASP
60
A
GLN
61
n
61
GLN
61
A
ILE
62
n
62
ILE
62
A
LEU
63
n
63
LEU
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
THR
82
n
82
THR
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
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
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
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
GLN
107
n
7
GLN
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
LEU
133
n
33
LEU
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
ILE
154
n
54
ILE
154
B
LYS
155
n
55
LYS
155
B
VAL
156
n
56
VAL
156
B
ARG
157
n
57
ARG
157
B
GLN
158
n
58
GLN
158
B
TYR
159
n
59
TYR
159
B
ASP
160
n
60
ASP
160
B
GLN
161
n
61
GLN
161
B
ILE
162
n
62
ILE
162
B
LEU
163
n
63
LEU
163
B
ILE
164
n
64
ILE
164
B
GLU
165
n
65
GLU
165
B
ILE
166
n
66
ILE
166
B
CYS
167
n
67
CYS
167
B
GLY
168
n
68
GLY
168
B
HIS
169
n
69
HIS
169
B
LYS
170
n
70
LYS
170
B
VAL
171
n
71
VAL
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
THR
182
n
82
THR
182
B
ASN
183
n
83
ASN
183
B
VAL
184
n
84
VAL
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
CYS
195
n
95
CYS
195
B
THR
196
n
96
THR
196
B
LEU
197
n
97
LEU
197
B
ASN
198
n
98
ASN
198
B
PHE
199
n
99
PHE
199
B
author_and_software_defined_assembly
PISA
2
dimeric
4320
-22
9040
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
N
ASN
198
B
N
ASN
98
A
O
THR
96
A
O
THR
96
A
O
LEU
97
A
O
LEU
97
B
N
ILE
103
B
N
ILE
3
A
O
VAL
11
A
O
VAL
11
A
N
ALA
22
A
N
ALA
22
A
O
LEU
23
A
O
LEU
23
A
N
ILE
85
A
N
ILE
85
A
N
THR
31
A
N
THR
31
A
O
THR
74
A
O
THR
74
A
O
VAL
77
A
O
VAL
77
A
N
ARG
57
A
N
ARG
57
A
O
GLU
65
A
O
GLU
65
A
N
LYS
14
A
N
LYS
14
A
N
ILE
15
A
N
ILE
15
A
O
GLN
18
A
O
GLN
18
A
N
THR
31
A
N
THR
31
A
O
THR
74
A
O
THR
74
A
O
VAL
77
A
O
VAL
77
A
N
ARG
57
A
N
ARG
57
A
N
GLN
58
A
N
GLN
58
A
O
LYS
43
A
O
LYS
43
B
O
VAL
111
B
O
VAL
11
B
N
ALA
122
B
N
ALA
22
B
O
LEU
123
B
O
LEU
23
B
N
ILE
185
B
N
ILE
85
B
N
THR
131
B
N
THR
31
B
O
THR
174
B
O
THR
74
B
O
VAL
177
B
O
VAL
77
B
N
ARG
157
B
N
ARG
57
B
O
GLU
165
B
O
GLU
65
B
N
LYS
114
B
N
LYS
14
B
N
ILE
115
B
N
ILE
15
B
O
GLN
118
B
O
GLN
18
B
N
THR
131
B
N
THR
31
B
O
THR
174
B
O
THR
74
B
O
VAL
177
B
O
VAL
77
B
N
ARG
157
B
N
ARG
57
B
N
GLN
158
B
N
GLN
58
B
O
LYS
143
B
O
LYS
43
1
-16.34
2.70
111.00
94.66
A
A
A
N
CA
C
ILE
ILE
ILE
50
50
50
B
N
1
B
GLU
134
-58.62
172.83
1
B
TRP
142
-171.07
-179.36
35.
0.252
0.203
0.208
0.208
2.20
33.
533
9504
9492
5.6
99.9
RANDOM
1
ISOTROPIC
THROUGHOUT EXCEPT LAST CYCLE
0.0
MOLECULAR REPLACEMENT
CNS
0.30
0.27
5.00
0.34
0.30
2.20
33.
86
1658
54
0
1518
0.012
1.60
1.60
26.47
1.10
1.598
1.5
2.632
2.0
2.277
2.0
3.471
2.5
0.3176
0.2959
2.27
10
31.8
2.20
33.0
1LZQ
9504
9492
0.0
0.0
0.079
1
6.5
99.9
0.449
2.20
2.26
3.3
1
100.0
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
refinement
CNS
1.0
Crystal structure of the complex of mutant HIV-1 protease (A71V, V82T, I84V) with an ethylenamine peptidomimetic inhibitor BOC-PHE-PSI[CH2CH2NH]-PHE-GLU-PHE-NH2
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
BIOLOGICAL ASSEMBLY IS A DIMER IN THE ASSYMETRIC UNIT
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
B
GLN
192
B
GLN
92
HELX_P
B
GLY
194
B
GLY
94
5
4
3
HYDROLASE/HYDROLASE INHIBITOR
HIV, PEPTIDOMIMETIC, ethylenamine ISOSTERE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
POL_HV1BR
UNP
1
501
P03367
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
501
599
1LZQ
1
99
P03367
A
1
1
99
501
599
1LZQ
101
199
P03367
B
1
1
99
1
ALA
engineered mutation
VAL
71
1LZQ
A
P03367
UNP
571
71
1
VAL
engineered mutation
THR
82
1LZQ
A
P03367
UNP
582
82
1
ILE
engineered mutation
VAL
84
1LZQ
A
P03367
UNP
584
84
2
ALA
engineered mutation
VAL
171
1LZQ
B
P03367
UNP
571
71
2
VAL
engineered mutation
THR
182
1LZQ
B
P03367
UNP
582
82
2
ILE
engineered mutation
VAL
184
1LZQ
B
P03367
UNP
584
84
4
3
5
4
3
5
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
anti-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
LEU
10
A
LEU
10
A
VAL
11
A
VAL
11
A
ALA
22
A
ALA
22
A
LEU
24
A
LEU
24
A
VAL
84
A
VAL
84
A
ILE
85
A
ILE
85
A
THR
31
A
THR
31
A
LEU
33
A
LEU
33
A
HIS
69
A
HIS
69
A
VAL
77
A
VAL
77
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
A
ILE
13
A
ILE
13
A
ILE
15
A
ILE
15
A
GLN
18
A
GLN
18
A
LEU
19
A
LEU
19
A
THR
31
A
THR
31
A
LEU
33
A
LEU
33
A
HIS
69
A
HIS
69
A
VAL
77
A
VAL
77
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
A
LYS
43
A
LYS
43
A
GLY
49
A
GLY
49
B
LEU
110
B
LEU
10
B
VAL
111
B
VAL
11
B
ALA
122
B
ALA
22
B
LEU
124
B
LEU
24
B
VAL
184
B
VAL
84
B
ILE
185
B
ILE
85
B
THR
131
B
THR
31
B
LEU
133
B
LEU
33
B
HIS
169
B
HIS
69
B
VAL
177
B
VAL
77
B
GLY
152
B
GLY
52
B
ILE
166
B
ILE
66
B
ILE
113
B
ILE
13
B
ILE
115
B
ILE
15
B
GLN
118
B
GLN
18
B
LEU
119
B
LEU
19
B
THR
131
B
THR
31
B
LEU
133
B
LEU
33
B
HIS
169
B
HIS
69
B
VAL
177
B
VAL
77
B
GLY
152
B
GLY
52
B
ILE
166
B
ILE
66
B
LYS
143
B
LYS
43
B
GLY
149
B
GLY
49
BINDING SITE FOR RESIDUE 0ZQ A 201
A
0ZQ
201
Software
29
BINDING SITE FOR RESIDUE BME A 387
A
BME
387
Software
4
A
ARG
8
A
ARG
8
29
1_555
A
ASP
25
A
ASP
25
29
1_555
A
GLY
27
A
GLY
27
29
1_555
A
ALA
28
A
ALA
28
29
1_555
A
ASP
29
A
ASP
29
29
1_555
A
ASP
30
A
ASP
30
29
1_555
A
VAL
32
A
VAL
32
29
1_555
A
ILE
47
A
ILE
47
29
1_555
A
GLY
48
A
GLY
48
29
1_555
A
GLY
49
A
GLY
49
29
1_555
A
ILE
50
A
ILE
50
29
1_555
A
PRO
81
A
PRO
81
29
1_555
A
THR
82
A
THR
82
29
1_555
A
HOH
370
E
HOH
29
1_555
B
ARG
108
B
ARG
8
29
1_555
B
ASP
125
B
ASP
25
29
1_555
B
GLY
127
B
GLY
27
29
1_555
B
ALA
128
B
ALA
28
29
1_555
B
ASP
129
B
ASP
29
29
1_555
B
ASP
130
B
ASP
30
29
1_555
B
VAL
132
B
VAL
32
29
1_555
B
ILE
147
B
ILE
47
29
1_555
B
GLY
148
B
GLY
48
29
1_555
B
GLY
149
B
GLY
49
29
1_555
B
ILE
150
B
ILE
50
29
1_555
B
PRO
181
B
PRO
81
29
1_555
B
THR
182
B
THR
82
29
1_555
B
HOH
319
F
HOH
29
1_555
B
HOH
331
F
HOH
29
1_555
A
TRP
6
A
TRP
6
4
1_555
B
ASP
129
B
ASP
29
4
1_555
B
ARG
187
B
ARG
87
4
1_555
B
ASN
188
B
ASN
88
4
1_555
169
hexagonal
P 61