0.015855
0.009154
0.000000
0.000000
0.018308
0.000000
0.000000
0.000000
0.011973
0.00000
0.00000
0.00000
Murthy, K.
Winborne, E.L.
Minnich, M.D.
Culp, J.S.
Debouck, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
63.070
63.070
83.520
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C19 H23 N O3
313.391
(2R,4S,5S)-5-amino-2-benzyl-4-hydroxy-6-phenylhexanoic acid
peptide-like
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
C6 H13 N O2
131.173
METHYL L-VALINATE
O-METHYLVALINE
peptide-like
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
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
N
262
N
H
N
263
N
H
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
N
N
274
S
C
N
275
S
C
N
276
N
O
N
277
N
C
Y
278
N
C
Y
279
N
C
Y
280
N
C
Y
281
N
C
Y
282
N
C
Y
283
N
C
N
284
N
C
N
285
R
C
N
286
N
C
N
287
N
O
N
288
N
C
Y
289
N
C
Y
290
N
C
Y
291
N
C
Y
292
N
C
Y
293
N
C
Y
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
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
N
N
320
S
C
N
321
N
C
N
322
N
O
N
323
N
C
N
324
N
C
N
325
N
C
N
326
N
O
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
N
N
337
S
C
N
338
N
C
N
339
N
O
N
340
N
C
N
341
N
O
N
342
N
O
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
N
N
351
S
C
N
352
N
C
N
353
N
O
N
354
R
C
N
355
N
O
N
356
N
C
N
357
N
O
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
N
N
368
S
C
N
369
N
C
N
370
N
O
N
371
N
C
Y
372
N
C
Y
373
N
C
Y
374
N
C
Y
375
N
N
Y
376
N
C
Y
377
N
C
Y
378
N
C
Y
379
N
C
Y
380
N
C
N
381
N
O
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
N
N
395
S
C
N
396
N
C
N
397
N
O
N
398
N
C
Y
399
N
C
Y
400
N
C
Y
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
C
N
405
N
O
N
406
N
O
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
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
N
C
N
423
N
C
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
H
N
436
N
H
N
437
N
N
N
438
S
C
N
439
N
C
N
440
N
O
N
441
N
C
N
442
N
C
N
443
N
C
N
444
N
C
N
445
N
O
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
H
N
458
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
Y
266
N
doub
Y
267
N
sing
Y
268
N
sing
Y
269
N
doub
Y
270
N
doub
Y
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
doub
N
276
N
sing
N
277
N
sing
Y
278
N
doub
Y
279
N
sing
Y
280
N
sing
Y
281
N
doub
Y
282
N
doub
Y
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
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
sing
N
311
N
sing
N
312
N
sing
N
313
N
doub
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
doub
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
doub
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
doub
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
Y
364
N
doub
Y
365
N
sing
Y
366
N
sing
N
367
N
sing
Y
368
N
doub
Y
369
N
sing
Y
370
N
sing
N
371
N
sing
Y
372
N
sing
Y
373
N
doub
N
374
N
sing
Y
375
N
doub
N
376
N
sing
Y
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
doub
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
Y
392
N
doub
Y
393
N
sing
Y
394
N
sing
N
395
N
sing
Y
396
N
doub
N
397
N
sing
Y
398
N
doub
N
399
N
sing
Y
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
doub
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
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
doub
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
267
22770
22778
1429626
The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations.
1992
10.2210/pdb1hef/pdb
pdb_00001hef
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
x-ray
1
1.0
10786.663
HIV-1 PROTEASE
1
man
polymer
667.835
SKF 108738 PEPTIDE INHIBITOR
1
syn
polymer
18.015
water
23
nat
water
no
no
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEENSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEENSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
E
polypeptide(L)
no
yes
AA(PJJ)V(VME)
AAXVX
I
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
n
n
n
n
n
Lentivirus
Escherichia
sample
11676
Human immunodeficiency virus 1
562
Escherichia coli
2.09
41.08
pdbx_database_status
struct_conf
struct_conf_type
atom_site
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
Derived calculations
Other
Atomic model
Data collection
Database references
Derived calculations
1
0
1994-05-31
1
1
2008-05-22
1
2
2011-07-13
1
3
2012-12-12
1
4
2017-11-29
2
0
2023-11-15
_pdbx_database_status.process_site
_atom_site.auth_atom_id
_atom_site.label_atom_id
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
HIV-1 PROTEASE IS A SYMMETRIC DIMER, WHILE THE INHIBITOR IS AN ASYMMETRIC MOLECULE. FURTHERMORE, THE INHIBITOR IS SMALL ENOUGH TO BE ENTIRELY CONTAINED WITHIN THE ACTIVE SITE OF THE ENZYME AND, THEREFORE, DOES NOT
CONTRIBUTE TO INTER-DIMER CONTACTS. THUS, OF THE TWO
POSSIBLE ORIENTATIONS OF THE INHIBITOR, NEITHER IS
THERMODYNAMICALLY PREFERRED. IN THE CRYSTAL STRUCTURE,
THEREFORE, BOTH ARE REPRESENTED EQUALLY. THE ASYMMETRIC UNIT OF THE CRYSTAL THUS CONSISTS OF ONE PROTEASE MONOMER, AND ONE COPY OF EACH OF TWO POSSIBLE ORIENTATIONS OF THE INHIBITOR. EACH COPY OF THE INHIBITOR REPRESENTS HALF THE TOTAL OCCUPANCY FOR THE INHIBITOR.
Y
BNL
1992-09-21
REL
HOH
water
THIS VARIANT OF THE HIV 1 PROTEASE HAS ASN AT THE POSITION 36 IN CHAIN E AS CONFIRMED BY INSPECTION OF THE ELECTRON DENSITY. SEE REFERENCES 14,15, AND 16 CITED IN J.BIOL.CHEM. V.267:22770, (1992).
Inhibitor
methyl N-{(2S,4S,5S)-5-[(L-alanyl-L-alanyl)amino]-2-benzyl-4-hydroxy-6-phenylhexanoyl}-L-valyl-L-valinate
Peptide-like
HOH
100
3
HOH
HOH
100
E
HOH
101
3
HOH
HOH
101
E
HOH
102
3
HOH
HOH
102
E
HOH
103
3
HOH
HOH
103
E
HOH
104
3
HOH
HOH
104
E
HOH
105
3
HOH
HOH
105
E
HOH
106
3
HOH
HOH
106
E
HOH
107
3
HOH
HOH
107
E
HOH
108
3
HOH
HOH
108
E
HOH
109
3
HOH
HOH
109
E
HOH
110
3
HOH
HOH
110
E
HOH
111
3
HOH
HOH
111
E
HOH
112
3
HOH
HOH
112
E
HOH
113
3
HOH
HOH
113
E
HOH
114
3
HOH
HOH
114
E
HOH
115
3
HOH
HOH
115
E
HOH
116
3
HOH
HOH
116
E
HOH
117
3
HOH
HOH
117
E
HOH
118
3
HOH
HOH
118
E
HOH
119
3
HOH
HOH
119
E
HOH
120
3
HOH
HOH
120
E
HOH
121
3
HOH
HOH
121
E
HOH
122
3
HOH
HOH
122
E
PRO
1
n
1
PRO
1
E
GLN
2
n
2
GLN
2
E
ILE
3
n
3
ILE
3
E
THR
4
n
4
THR
4
E
LEU
5
n
5
LEU
5
E
TRP
6
n
6
TRP
6
E
GLN
7
n
7
GLN
7
E
ARG
8
n
8
ARG
8
E
PRO
9
n
9
PRO
9
E
LEU
10
n
10
LEU
10
E
VAL
11
n
11
VAL
11
E
THR
12
n
12
THR
12
E
ILE
13
n
13
ILE
13
E
LYS
14
n
14
LYS
14
E
ILE
15
n
15
ILE
15
E
GLY
16
n
16
GLY
16
E
GLY
17
n
17
GLY
17
E
GLN
18
n
18
GLN
18
E
LEU
19
n
19
LEU
19
E
LYS
20
n
20
LYS
20
E
GLU
21
n
21
GLU
21
E
ALA
22
n
22
ALA
22
E
LEU
23
n
23
LEU
23
E
LEU
24
n
24
LEU
24
E
ASP
25
n
25
ASP
25
E
THR
26
n
26
THR
26
E
GLY
27
n
27
GLY
27
E
ALA
28
n
28
ALA
28
E
ASP
29
n
29
ASP
29
E
ASP
30
n
30
ASP
30
E
THR
31
n
31
THR
31
E
VAL
32
n
32
VAL
32
E
LEU
33
n
33
LEU
33
E
GLU
34
n
34
GLU
34
E
GLU
35
n
35
GLU
35
E
ASN
36
n
36
ASN
36
E
SER
37
n
37
SER
37
E
LEU
38
n
38
LEU
38
E
PRO
39
n
39
PRO
39
E
GLY
40
n
40
GLY
40
E
ARG
41
n
41
ARG
41
E
TRP
42
n
42
TRP
42
E
LYS
43
n
43
LYS
43
E
PRO
44
n
44
PRO
44
E
LYS
45
n
45
LYS
45
E
MET
46
n
46
MET
46
E
ILE
47
n
47
ILE
47
E
GLY
48
n
48
GLY
48
E
GLY
49
n
49
GLY
49
E
ILE
50
n
50
ILE
50
E
GLY
51
n
51
GLY
51
E
GLY
52
n
52
GLY
52
E
PHE
53
n
53
PHE
53
E
ILE
54
n
54
ILE
54
E
LYS
55
n
55
LYS
55
E
VAL
56
n
56
VAL
56
E
ARG
57
n
57
ARG
57
E
GLN
58
n
58
GLN
58
E
TYR
59
n
59
TYR
59
E
ASP
60
n
60
ASP
60
E
GLN
61
n
61
GLN
61
E
ILE
62
n
62
ILE
62
E
LEU
63
n
63
LEU
63
E
ILE
64
n
64
ILE
64
E
GLU
65
n
65
GLU
65
E
ILE
66
n
66
ILE
66
E
CYS
67
n
67
CYS
67
E
GLY
68
n
68
GLY
68
E
HIS
69
n
69
HIS
69
E
LYS
70
n
70
LYS
70
E
ALA
71
n
71
ALA
71
E
ILE
72
n
72
ILE
72
E
GLY
73
n
73
GLY
73
E
THR
74
n
74
THR
74
E
VAL
75
n
75
VAL
75
E
LEU
76
n
76
LEU
76
E
VAL
77
n
77
VAL
77
E
GLY
78
n
78
GLY
78
E
PRO
79
n
79
PRO
79
E
THR
80
n
80
THR
80
E
PRO
81
n
81
PRO
81
E
VAL
82
n
82
VAL
82
E
ASN
83
n
83
ASN
83
E
ILE
84
n
84
ILE
84
E
ILE
85
n
85
ILE
85
E
GLY
86
n
86
GLY
86
E
ARG
87
n
87
ARG
87
E
ASN
88
n
88
ASN
88
E
LEU
89
n
89
LEU
89
E
LEU
90
n
90
LEU
90
E
THR
91
n
91
THR
91
E
GLN
92
n
92
GLN
92
E
ILE
93
n
93
ILE
93
E
GLY
94
n
94
GLY
94
E
CYS
95
n
95
CYS
95
E
THR
96
n
96
THR
96
E
LEU
97
n
97
LEU
97
E
ASN
98
n
98
ASN
98
E
PHE
99
n
99
PHE
99
E
ALA
201
n
1
ALA
201
I
ALA
202
n
2
ALA
202
I
PS0
205
n
3
PJJ
205
I
VAL
210
n
4
VAL
210
I
VME
211
n
5
VME
211
I
author_defined_assembly
4
tetrameric
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
-0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
9_555
-x,-x+y,-z+2/3
crystal symmetry operation
0.0000000000
0.0000000000
55.6800000000
1
E
HOH
100
C
HOH
1
E
I
OD2
N
ASP
ALA
29
201
2.03
1
E
E
OE1
O
GLN
HOH
7
116
2.14
1
E
E
NE1
O
TRP
HOH
6
113
2.15
1
E
E
NH1
O
ARG
HOH
41
118
2.19
1
I
I
ALA
PJJ
202
205
111.56
1
14.39
1.90
111.40
125.79
E
E
E
CB
CA
C
VAL
VAL
VAL
11
11
11
N
1
7.99
0.90
118.30
126.29
E
E
E
CB
CG
OD2
ASP
ASP
ASP
25
25
25
N
1
20.13
2.70
114.20
134.33
E
E
E
CB
CG
CD
GLU
GLU
GLU
34
34
34
N
1
-15.13
2.30
121.90
106.77
E
E
E
OD1
CG
ND2
ASN
ASN
ASN
36
36
36
N
1
-15.36
2.10
120.10
104.74
E
E
E
CA
C
O
ILE
ILE
ILE
50
50
50
N
1
25.85
2.00
116.20
142.05
E
E
E
CA
C
N
ILE
ILE
GLY
50
50
51
Y
1
9.83
1.40
123.60
133.43
E
E
E
CD
NE
CZ
ARG
ARG
ARG
57
57
57
N
1
-8.13
1.10
119.40
111.27
E
E
E
NH1
CZ
NH2
ARG
ARG
ARG
57
57
57
N
1
8.76
0.50
120.30
129.06
E
E
E
NE
CZ
NH2
ARG
ARG
ARG
57
57
57
N
1
15.63
1.80
110.60
126.23
E
E
E
N
CA
CB
GLN
GLN
GLN
58
58
58
N
1
17.19
2.20
113.40
130.59
E
E
E
CA
CB
CG
GLN
GLN
GLN
58
58
58
N
1
-9.28
1.40
123.60
114.32
E
E
E
CD
NE
CZ
ARG
ARG
ARG
87
87
87
N
1
-6.27
0.50
120.30
114.03
E
E
E
NE
CZ
NH1
ARG
ARG
ARG
87
87
87
N
1
14.77
2.30
115.30
130.07
E
E
E
CA
CB
CG
LEU
LEU
LEU
97
97
97
N
1
29.70
2.50
121.70
151.40
I
I
I
C
N
CA
ALA
ALA
ALA
201
202
202
Y
1
16.81
2.50
121.70
138.51
I
I
I
C
N
CA
VAL
VME
VME
210
211
211
Y
1
E
E
CE
CE1
MET
PHE
46
53
1.59
1_555
10_555
1
E
I
OD2
CG1
ASP
VME
29
211
1.94
1_555
9_555
1
E
E
OE1
N
GLN
GLY
2
40
1.95
1_555
3_564
1
E
E
CE
CD1
MET
PHE
46
53
2.10
1_555
10_555
1
E
I
OD2
CM
ASP
VME
29
211
2.10
1_555
9_555
1
E
E
ND2
ND2
ASN
ASN
98
98
2.13
1_555
9_555
1
E
E
CD1
O
LEU
HOH
10
105
2.14
1_555
11_555
1
E
E
OG
O
SER
HOH
37
113
2.18
1_555
2_665
THE INHIBITOR ALA-ALA-PJJ-VAL-VME IS DISORDERED AROUND THE TWO-FOLD CYRSTALLOGRAPHIC AXIS. APPLICATION OF CRYSTALLOGRAPHIC SYMMETRY RESULTS IN THE OVERLAP OF THE TWO ORIENTATIONS. THE OCCUPANCY OF EACH ORIENTATION IS 1/2.
0.159
2.20
5.0
3649
1
2.0
2.20
5.0
23
829
0
0
806
0.020
0.025
0.044
0.050
0.055
0.060
0.219
0.200
1.7
2.0
23.7
15.0
30.0
25.0
refinement
PROLSQ
The crystal structures at 2.2 angstroms resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations
1
N
N
2
N
N
3
N
N
E
GLY
86
A
GLY
86
HELX_P
ONLY HELIX IN STRUCTURE
E
GLY
94
A
GLY
94
1
1
9
covale
1.312
both
I
ALA
202
B
C
ALA
2
1_555
I
PJJ
205
B
N
PJJ
3
1_555
covale
1.344
both
I
PJJ
205
B
C
PJJ
3
1_555
I
VAL
210
B
N
VAL
4
1_555
covale
1.304
both
I
VAL
210
B
C
VAL
4
1_555
I
VME
211
B
N
VME
5
1_555
HYDROLASE/HYDROLASE INHIBITOR
HYDROLASE-HYDROLASE INHIBITOR COMPLEX
POL_HV1B1
UNP
1
1
P03366
FFREDLAFLQGKAREFSSEQTRANSPTISSEQTRANSPTRRELQVWGRDNNSPSEAGADRQGTVSFNFPQITLWQRPLVT
IKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQ
IGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRK
LVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGW
KGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYE
LHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEP
VHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPI
QKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTT
NQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVS
AGIRKILFLDGIDKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVI
LVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTSATVKAACWWAGIKQEFGIPYNPQSQGVVES
MNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRNP
LWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED
1HEF
PDB
2
1
1HEF
AA(PJJ)V(VME)
69
167
1HEF
1
99
P03366
E
1
1
99
201
211
1HEF
201
211
1HEF
I
2
1
5
1
MET
conflict
ASN
36
1HEF
E
P03366
UNP
104
36
8
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
E
LYS
43
A
LYS
43
E
GLY
49
A
GLY
49
E
GLY
52
A
GLY
52
E
ILE
66
A
ILE
66
E
HIS
69
A
HIS
69
E
GLY
78
A
GLY
78
E
THR
31
A
THR
31
E
GLU
34
A
GLU
34
E
ASN
83
A
ASN
83
E
ILE
85
A
ILE
85
E
GLN
18
A
GLN
18
E
ASP
25
A
ASP
25
E
PRO
9
A
PRO
9
E
ILE
15
A
ILE
15
E
GLU
65
A
GLU
65
E
ILE
66
A
ILE
66
BINDING SITE FOR CHAIN I OF SKF 108738 PEPTIDE INHIBITOR
Software
22
E
ARG
8
A
ARG
8
22
1_555
E
ASP
25
A
ASP
25
22
9_555
E
ASP
25
A
ASP
25
22
1_555
E
GLY
27
A
GLY
27
22
1_555
E
GLY
27
A
GLY
27
22
9_555
E
ALA
28
A
ALA
28
22
1_555
E
ALA
28
A
ALA
28
22
9_555
E
ASP
29
A
ASP
29
22
1_555
E
ASP
29
A
ASP
29
22
9_555
E
ILE
47
A
ILE
47
22
9_555
E
GLY
48
A
GLY
48
22
9_555
E
GLY
48
A
GLY
48
22
1_555
E
GLY
49
A
GLY
49
22
1_555
E
GLY
49
A
GLY
49
22
9_555
E
ILE
50
A
ILE
50
22
1_555
E
ILE
50
A
ILE
50
22
9_555
E
PRO
81
A
PRO
81
22
1_555
E
VAL
82
A
VAL
82
22
1_555
E
VAL
82
A
VAL
82
22
9_555
E
ILE
84
A
ILE
84
22
9_555
E
HOH
100
C
HOH
22
9_555
E
HOH
100
C
HOH
22
1_555
178
P 61 2 2