0.016028
0.009254
0.000000
0.000000
0.018508
0.000000
0.000000
0.000000
0.012186
0.00000
0.00000
0.00000
Stout, C.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
62.390
62.390
82.060
C50 H64 N6 O10
909.077
benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate
TL-3, C2 symmetric inhibitor
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
C2 H6 O S
78.133
DIMETHYL SULFOXIDE
non-polymer
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
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
C
N
2
N
O
N
3
N
O
N
4
N
C
Y
5
N
C
Y
6
N
C
Y
7
N
C
Y
8
N
C
Y
9
N
C
Y
10
N
C
N
11
N
N
N
12
S
C
N
13
N
C
N
14
N
O
N
15
N
C
N
16
N
N
N
17
S
C
N
18
N
C
N
19
N
O
N
20
N
C
N
21
N
C
N
22
N
C
N
23
R
C
N
24
N
O
N
25
S
C
N
26
N
N
N
27
N
C
Y
28
N
C
Y
29
N
C
Y
30
N
C
Y
31
N
C
Y
32
N
C
Y
33
N
C
N
34
N
N
N
35
S
C
N
36
R
C
N
37
N
O
N
38
N
C
Y
39
N
C
Y
40
N
C
Y
41
N
C
Y
42
N
C
Y
43
N
C
Y
44
N
C
N
45
N
N
N
46
S
C
N
47
N
C
N
48
N
O
N
49
N
C
N
50
N
C
N
51
N
C
N
52
N
N
N
53
S
C
N
54
N
C
N
55
N
O
N
56
N
C
N
57
N
C
N
58
N
O
N
59
N
O
N
60
N
C
Y
61
N
C
Y
62
N
C
Y
63
N
C
Y
64
N
C
Y
65
N
C
Y
66
N
C
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
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
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
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
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
N
N
132
S
C
N
133
N
C
N
134
N
O
N
135
N
C
N
136
N
O
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
N
N
145
S
C
N
146
N
C
N
147
N
O
N
148
N
C
N
149
N
C
N
150
N
C
N
151
N
N
N
152
N
C
N
153
N
N
N
154
N
N
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
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
N
N
172
S
C
N
173
N
C
N
174
N
O
N
175
N
C
N
176
N
C
N
177
N
O
N
178
N
N
N
179
N
O
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
N
N
189
S
C
N
190
N
C
N
191
N
O
N
192
N
C
N
193
N
C
N
194
N
O
N
195
N
O
N
196
N
O
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
C
N
205
N
C
N
206
N
O
N
207
N
S
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
N
N
215
R
C
N
216
N
C
N
217
N
O
N
218
N
C
N
219
N
S
N
220
N
O
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
S
N
229
N
O
N
230
N
C
N
231
N
C
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
N
N
239
S
C
N
240
N
C
N
241
N
O
N
242
N
C
N
243
N
C
N
244
N
C
N
245
N
O
N
246
N
N
N
247
N
O
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
N
N
259
S
C
N
260
N
C
N
261
N
O
N
262
N
C
N
263
N
C
N
264
N
C
N
265
N
O
N
266
N
O
N
267
N
O
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
H
N
276
N
H
N
277
N
N
N
278
N
C
N
279
N
C
N
280
N
O
N
281
N
O
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
N
C
Y
292
N
C
Y
293
N
N
Y
294
N
C
Y
295
N
C
Y
296
N
N
N
297
N
O
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
O
N
309
N
H
N
310
N
H
N
311
N
N
N
312
S
C
N
313
N
C
N
314
N
O
N
315
S
C
N
316
N
C
N
317
N
C
N
318
N
C
N
319
N
O
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
N
N
334
S
C
N
335
N
C
N
336
N
O
N
337
N
C
N
338
N
C
N
339
N
C
N
340
N
C
N
341
N
O
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
N
N
356
S
C
N
357
N
C
N
358
N
O
N
359
N
C
N
360
N
C
N
361
N
C
N
362
N
C
N
363
N
N
N
364
N
O
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
N
N
381
S
C
N
382
N
C
N
383
N
O
N
384
N
C
N
385
N
C
N
386
N
S
N
387
N
C
N
388
N
O
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
N
N
401
S
C
N
402
N
C
N
403
N
O
N
404
N
C
Y
405
N
C
Y
406
N
C
Y
407
N
C
Y
408
N
C
Y
409
N
C
Y
410
N
C
N
411
N
O
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
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
N
N
424
S
C
N
425
N
C
N
426
N
O
N
427
N
C
N
428
N
C
N
429
N
C
N
430
N
O
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
N
N
441
S
C
N
442
N
C
N
443
N
O
N
444
R
C
N
445
N
O
N
446
N
C
N
447
N
O
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
N
Y
466
N
C
Y
467
N
C
Y
468
N
C
Y
469
N
C
Y
470
N
C
N
471
N
O
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
N
N
485
S
C
N
486
N
C
N
487
N
O
N
488
N
C
Y
489
N
C
Y
490
N
C
Y
491
N
C
Y
492
N
C
Y
493
N
C
Y
494
N
C
N
495
N
O
N
496
N
O
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
505
N
H
N
506
N
H
N
507
N
H
N
508
N
N
N
509
S
C
N
510
N
C
N
511
N
O
N
512
N
C
N
513
N
C
N
514
N
C
N
515
N
O
N
516
N
H
N
517
N
H
N
518
N
H
N
519
N
H
N
520
N
H
N
521
N
H
N
522
N
H
N
523
N
H
N
524
N
H
N
525
N
H
N
526
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
Y
8
N
doub
Y
9
N
sing
Y
10
N
sing
N
11
N
sing
Y
12
N
doub
N
13
N
sing
Y
14
N
sing
N
15
N
sing
Y
16
N
doub
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
doub
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
sing
N
34
N
doub
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
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
Y
57
N
doub
Y
58
N
sing
Y
59
N
sing
N
60
N
sing
Y
61
N
doub
N
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
sing
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
sing
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
Y
80
N
doub
Y
81
N
sing
Y
82
N
sing
N
83
N
sing
Y
84
N
doub
N
85
N
sing
Y
86
N
doub
N
87
N
sing
Y
88
N
sing
N
89
N
sing
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
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
doub
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
Y
123
N
doub
Y
124
N
sing
Y
125
N
sing
N
126
N
sing
Y
127
N
doub
N
128
N
sing
Y
129
N
sing
N
130
N
sing
Y
131
N
doub
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
doub
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
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
doub
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
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
doub
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
doub
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
doub
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
doub
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
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
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
doub
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
doub
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
doub
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
doub
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
doub
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
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
doub
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
Y
291
N
sing
Y
292
N
doub
Y
293
N
doub
N
294
N
sing
Y
295
N
sing
N
296
N
sing
Y
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
doub
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
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
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
doub
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
doub
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
doub
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
Y
399
N
doub
Y
400
N
sing
Y
401
N
sing
N
402
N
sing
Y
403
N
doub
N
404
N
sing
Y
405
N
doub
N
406
N
sing
Y
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
doub
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
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
doub
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
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
Y
460
N
sing
Y
461
N
sing
N
462
N
sing
Y
463
N
sing
Y
464
N
doub
N
465
N
sing
Y
466
N
doub
N
467
N
sing
Y
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
doub
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
Y
483
N
doub
Y
484
N
sing
Y
485
N
sing
N
486
N
sing
Y
487
N
doub
N
488
N
sing
Y
489
N
doub
N
490
N
sing
Y
491
N
sing
N
492
N
sing
N
493
N
sing
N
494
N
sing
N
495
N
sing
N
496
N
sing
N
497
N
sing
N
498
N
sing
N
499
N
sing
N
500
N
sing
N
501
N
sing
N
502
N
doub
N
503
N
sing
N
504
N
sing
N
505
N
sing
N
506
N
sing
N
507
N
sing
N
508
N
sing
N
509
N
sing
N
510
N
sing
N
511
N
sing
N
512
N
sing
N
513
N
sing
US
Chem.Biol.Drug Des.
1747-0277
75
257
268
10.1111/j.1747-0285.2009.00943.x
20659109
Fragment-based screen against HIV protease.
2010
10.2210/pdb3kfp/pdb
pdb_00003kfp
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
100
1
Rh coated flat mirror
CCD
2009-04-07
ADSC QUANTUM 315r
Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
SINGLE WAVELENGTH
M
x-ray
1
0.97946
1.0
BL7-1
SSRL
0.97946
SYNCHROTRON
SSRL BEAMLINE BL7-1
10831.833
Protease
3.4.23.16
1
man
polymer
909.077
benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate
1
syn
non-polymer
78.133
DIMETHYL SULFOXIDE
3
syn
non-polymer
78.133
BETA-MERCAPTOETHANOL
1
syn
non-polymer
18.015
water
100
nat
water
no
no
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
A
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
R8
sample
POL
11676
Human immunodeficiency virus 1
562
Escherichia coli
BL21.DE3
PLASMID
PET 21A+
1
2.13
42.20
VAPOR DIFFUSION
5.8
0.5 M KSCN, 0.1 M MES-HCL, pH 5.8, 10% DMSO, VAPOR DIFFUSION, temperature 277K
277
database_2
pdbx_unobs_or_zero_occ_atoms
struct_conn
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
Advisory
Database references
Derived calculations
Data collection
Refinement description
1
0
2010-02-23
1
1
2011-07-13
1
2
2013-02-27
1
3
2021-10-13
1
4
2023-09-06
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_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 NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, WILD TYPE
HIV Protease with fragment 4D9 bound
HIV Protease (PR) dimer without inhibitor; acetate in exo site
HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking
HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 1F1 in the outside/top of flap
HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 2F4 in the outside/top of flap
RCSB
Y
RCSB
2009-10-27
REL
REL
3TL
benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate
DMS
DIMETHYL SULFOXIDE
BME
BETA-MERCAPTOETHANOL
HOH
water
IN THIS STRUCTURE THE INHIBITOR TL-3 (PDB LIGAND 3TL) IS BOUND TO HIV-1 PROTEASE DIMER. BECAUSE TL-3 HAS INTERNAL 2-FOLD SYMMETRY, ONLY ONE-HALF OF THE INHIBITOR (PDB LIGAND INT) IS PRESENT IN THE ASYMMETRIC UNIT. 2-FOLD ROTATION GENERATES A FULL TL-3 INHIBITOR WITH A BOND BETWEEN C2-C2. THE LONG C2-C2 BOND IN THIS STRUCTURE (2.41 A RATHER THAN 1.54 A) IS DUE TO ERROR IN REFINEMENT
2AZ8
HIV Protease monomer in 2AZ8
PDB
experimental model
Inhibitor
N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide
Peptide-like
3TL
200
2
3TL
3TL
200
A
DMS
300
3
DMS
DMS
300
A
DMS
301
3
DMS
DMS
301
A
DMS
302
3
DMS
DMS
302
A
BME
303
4
BME
BME
303
A
HOH
305
5
HOH
HOH
305
A
HOH
306
5
HOH
HOH
306
A
HOH
307
5
HOH
HOH
307
A
HOH
309
5
HOH
HOH
309
A
HOH
310
5
HOH
HOH
310
A
HOH
312
5
HOH
HOH
312
A
HOH
313
5
HOH
HOH
313
A
HOH
314
5
HOH
HOH
314
A
HOH
315
5
HOH
HOH
315
A
HOH
316
5
HOH
HOH
316
A
HOH
317
5
HOH
HOH
317
A
HOH
318
5
HOH
HOH
318
A
HOH
319
5
HOH
HOH
319
A
HOH
320
5
HOH
HOH
320
A
HOH
321
5
HOH
HOH
321
A
HOH
322
5
HOH
HOH
322
A
HOH
324
5
HOH
HOH
324
A
HOH
325
5
HOH
HOH
325
A
HOH
326
5
HOH
HOH
326
A
HOH
327
5
HOH
HOH
327
A
HOH
328
5
HOH
HOH
328
A
HOH
329
5
HOH
HOH
329
A
HOH
330
5
HOH
HOH
330
A
HOH
332
5
HOH
HOH
332
A
HOH
333
5
HOH
HOH
333
A
HOH
334
5
HOH
HOH
334
A
HOH
335
5
HOH
HOH
335
A
HOH
336
5
HOH
HOH
336
A
HOH
337
5
HOH
HOH
337
A
HOH
338
5
HOH
HOH
338
A
HOH
339
5
HOH
HOH
339
A
HOH
340
5
HOH
HOH
340
A
HOH
342
5
HOH
HOH
342
A
HOH
343
5
HOH
HOH
343
A
HOH
344
5
HOH
HOH
344
A
HOH
345
5
HOH
HOH
345
A
HOH
346
5
HOH
HOH
346
A
HOH
347
5
HOH
HOH
347
A
HOH
348
5
HOH
HOH
348
A
HOH
349
5
HOH
HOH
349
A
HOH
351
5
HOH
HOH
351
A
HOH
352
5
HOH
HOH
352
A
HOH
353
5
HOH
HOH
353
A
HOH
354
5
HOH
HOH
354
A
HOH
355
5
HOH
HOH
355
A
HOH
356
5
HOH
HOH
356
A
HOH
357
5
HOH
HOH
357
A
HOH
358
5
HOH
HOH
358
A
HOH
359
5
HOH
HOH
359
A
HOH
360
5
HOH
HOH
360
A
HOH
361
5
HOH
HOH
361
A
HOH
362
5
HOH
HOH
362
A
HOH
363
5
HOH
HOH
363
A
HOH
364
5
HOH
HOH
364
A
HOH
365
5
HOH
HOH
365
A
HOH
366
5
HOH
HOH
366
A
HOH
367
5
HOH
HOH
367
A
HOH
368
5
HOH
HOH
368
A
HOH
369
5
HOH
HOH
369
A
HOH
370
5
HOH
HOH
370
A
HOH
371
5
HOH
HOH
371
A
HOH
372
5
HOH
HOH
372
A
HOH
373
5
HOH
HOH
373
A
HOH
374
5
HOH
HOH
374
A
HOH
375
5
HOH
HOH
375
A
HOH
376
5
HOH
HOH
376
A
HOH
377
5
HOH
HOH
377
A
HOH
378
5
HOH
HOH
378
A
HOH
379
5
HOH
HOH
379
A
HOH
380
5
HOH
HOH
380
A
HOH
381
5
HOH
HOH
381
A
HOH
382
5
HOH
HOH
382
A
HOH
383
5
HOH
HOH
383
A
HOH
384
5
HOH
HOH
384
A
HOH
385
5
HOH
HOH
385
A
HOH
386
5
HOH
HOH
386
A
HOH
387
5
HOH
HOH
387
A
HOH
388
5
HOH
HOH
388
A
HOH
389
5
HOH
HOH
389
A
HOH
390
5
HOH
HOH
390
A
HOH
391
5
HOH
HOH
391
A
HOH
392
5
HOH
HOH
392
A
HOH
393
5
HOH
HOH
393
A
HOH
394
5
HOH
HOH
394
A
HOH
395
5
HOH
HOH
395
A
HOH
396
5
HOH
HOH
396
A
HOH
397
5
HOH
HOH
397
A
HOH
398
5
HOH
HOH
398
A
HOH
399
5
HOH
HOH
399
A
HOH
400
5
HOH
HOH
400
A
HOH
401
5
HOH
HOH
401
A
HOH
402
5
HOH
HOH
402
A
HOH
403
5
HOH
HOH
403
A
HOH
404
5
HOH
HOH
404
A
HOH
405
5
HOH
HOH
405
A
HOH
406
5
HOH
HOH
406
A
HOH
407
5
HOH
HOH
407
A
HOH
408
5
HOH
HOH
408
A
HOH
409
5
HOH
HOH
409
A
HOH
410
5
HOH
HOH
410
A
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
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
ASN
37
n
37
ASN
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
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
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
software_defined_assembly
PISA
2
dimeric
3830
-25.3
9640
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
7_555
y,x,-z+1/3
crystal symmetry operation
0.0000000000
0.0000000000
27.3533333333
A
N
LYS
45
A
N
LYS
45
A
O
VAL
56
A
O
VAL
56
A
N
TYR
59
A
N
TYR
59
A
O
VAL
75
A
O
VAL
75
A
O
LEU
76
A
O
LEU
76
A
N
LEU
33
A
N
LEU
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
ALA
22
A
O
ALA
22
A
N
VAL
11
A
N
VAL
11
A
N
LYS
14
A
N
LYS
14
A
O
GLU
65
A
O
GLU
65
1
A
HOH
306
G
HOH
1
A
HOH
342
G
HOH
1
A
A
C2
O
DMS
HOH
302
305
2.01
1
A
A
NH2
O
ARG
HOH
8
383
2.13
1
A
A
GLY
ARG
40
41
-148.52
1
7.41
1.20
111.50
118.91
A
A
A
CB
CA
C
CYS
CYS
CYS
67
67
67
N
1
A
A
CB
CG
TRP
TRP
6
6
-0.127
0.018
1.498
1.371
N
1
A
A
CB
SG
CYS
CYS
67
67
-0.111
0.016
1.812
1.701
N
1
A
A
O
O
HOH
HOH
383
383
2.19
1_555
11_555
1
A
A
O
O
HOH
HOH
346
346
2.19
1_555
12_545
1
A
GLU
34
-48.75
156.08
1
A
MET
36
-170.19
142.83
1
A
PRO
39
-37.16
109.29
1
A
PRO
79
-76.12
43.68
38.229
0.50
0.25
0.00
0.50
0.00
-0.74
0.954
0.915
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.31318
0.22571
0.22969
1.77
32.67
462
9716
9095
4.8
97.67
1.00
0.50
4.53
0.14
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.16
0.17
0.80
0.80
1.20
HIV Protease monomer in 2AZ8
MAXIMUM LIKELIHOOD
MASK
1.77
32.67
100
908
49
0
759
0.023
0.02
916
1.987
1.99
1399
7.159
7.50
196
41.771
24.81
27
17.999
15.00
144
15.335
15.00
4
0.139
0.20
128
0.008
0.02
986
0.290
0.274
1.812
44
635
20
97.14
1.77
54.03
3KFP
9716
9561
0.0
0.0
0.099
0.099
1
4.1
6.5
98.4
0.734
1.77
1.81
0.8
0.734
1
6.7
98.1
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.5.0090
data extraction
PDB
help@deposit.rcsb.org
June 11, 2008
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.005
data collection
Blu-Ice
data reduction
MOSFLM
data scaling
SCALA
phasing
MOLREP
HIV Protease (PR) with inhibitor TL-3 bound, and DMSOs in exo site
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
4
N
N
5
N
N
A
GLY
86
A
GLY
86
HELX_P
A
THR
91
A
THR
91
1
1
6
covale
2.020
none
A
CYS
67
A
SG
CYS
67
1_555
A
BME
303
F
S2
BME
1_555
covale
2.407
none
A
3TL
200
B
C2
3TL
1_555
A
3TL
200
B
C2
3TL
7_555
HYDROLASE/HYDROLASE INHIBITOR
HIV-1, PROTEASE, EXO SITE, Aspartyl protease, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Q903N5_9HIV1
UNP
1
1
Q903N5
PQITLWRRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
1
99
3KFP
1
99
Q903N5
A
1
1
99
1
ARG
engineered mutation
LYS
7
3KFP
A
Q903N5
UNP
7
7
8
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
LYS
43
A
LYS
43
A
GLY
49
A
GLY
49
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
A
HIS
69
A
HIS
69
A
VAL
77
A
VAL
77
A
VAL
32
A
VAL
32
A
LEU
33
A
LEU
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
BINDING SITE FOR RESIDUE 3TL A 200
A
3TL
200
Software
15
BINDING SITE FOR RESIDUE DMS A 300
A
DMS
300
Software
7
BINDING SITE FOR RESIDUE DMS A 301
A
DMS
301
Software
5
BINDING SITE FOR RESIDUE DMS A 302
A
DMS
302
Software
7
BINDING SITE FOR RESIDUE BME A 303
A
BME
303
Software
3
A
ARG
8
A
ARG
8
15
7_555
A
ASP
25
A
ASP
25
15
1_555
A
ASP
25
A
ASP
25
15
7_555
A
GLY
27
A
GLY
27
15
1_555
A
ALA
28
A
ALA
28
15
1_555
A
ASP
29
A
ASP
29
15
1_555
A
ILE
47
A
ILE
47
15
1_555
A
GLY
48
A
GLY
48
15
1_555
A
GLY
49
A
GLY
49
15
1_555
A
ILE
50
A
ILE
50
15
1_555
A
PRO
81
A
PRO
81
15
7_555
A
VAL
82
A
VAL
82
15
7_555
A
ILE
84
A
ILE
84
15
1_555
A
HOH
306
G
HOH
15
7_555
A
HOH
306
G
HOH
15
1_555
A
THR
12
A
THR
12
7
1_555
A
THR
12
A
THR
12
7
12_545
A
LYS
14
A
LYS
14
7
1_555
A
GLU
65
A
GLU
65
7
1_555
A
ILE
66
A
ILE
66
7
1_555
A
CYS
67
A
CYS
67
7
1_555
A
GLY
68
A
GLY
68
7
1_555
A
PRO
39
A
PRO
39
5
1_555
A
ILE
62
A
ILE
62
5
1_555
A
LEU
63
A
LEU
63
5
1_555
A
DMS
302
E
DMS
5
1_555
A
HOH
305
G
HOH
5
1_555
A
LYS
14
A
LYS
14
7
1_555
A
ILE
15
A
ILE
15
7
1_555
A
GLY
16
A
GLY
16
7
1_555
A
GLY
17
A
GLY
17
7
1_555
A
LEU
63
A
LEU
63
7
1_555
A
DMS
301
D
DMS
7
1_555
A
HOH
305
G
HOH
7
1_555
A
VAL
11
A
VAL
11
3
1_555
A
THR
12
A
THR
12
3
1_555
A
CYS
67
A
CYS
67
3
1_555
178
P 61 2 2