0.015990
0.009232
0.000000
0.000000
0.018464
0.000000
0.000000
0.000000
0.012217
0.00000
0.00000
0.00000
Heaslet, H.
Kutilek, V.
Morris, G.M.
Lin, Y.-C.
Elder, J.H.
Torbett, B.E.
Stout, C.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
62.539
62.539
81.852
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
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
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
N
N
205
R
C
N
206
N
C
N
207
N
O
N
208
N
C
N
209
N
S
N
210
N
O
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
N
N
219
S
C
N
220
N
C
N
221
N
O
N
222
N
C
N
223
N
C
N
224
N
C
N
225
N
O
N
226
N
N
N
227
N
O
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
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
O
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
N
N
258
N
C
N
259
N
C
N
260
N
O
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
N
N
268
S
C
N
269
N
C
N
270
N
O
N
271
N
C
Y
272
N
C
Y
273
N
N
Y
274
N
C
Y
275
N
C
Y
276
N
N
N
277
N
O
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
O
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
S
C
N
296
N
C
N
297
N
C
N
298
N
C
N
299
N
O
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
N
N
314
S
C
N
315
N
C
N
316
N
O
N
317
N
C
N
318
N
C
N
319
N
C
N
320
N
C
N
321
N
O
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
H
N
334
N
H
N
335
N
N
N
336
S
C
N
337
N
C
N
338
N
O
N
339
N
C
N
340
N
C
N
341
N
C
N
342
N
C
N
343
N
N
N
344
N
O
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
N
N
361
S
C
N
362
N
C
N
363
N
O
N
364
N
C
N
365
N
C
N
366
N
S
N
367
N
C
N
368
N
O
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
Y
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
Y
390
N
C
N
391
N
O
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
N
N
404
S
C
N
405
N
C
N
406
N
O
N
407
N
C
N
408
N
C
N
409
N
C
N
410
N
O
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
N
N
421
S
C
N
422
N
C
N
423
N
O
N
424
N
C
N
425
N
O
N
426
N
O
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
N
N
435
S
C
N
436
N
C
N
437
N
O
N
438
R
C
N
439
N
O
N
440
N
C
N
441
N
O
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
H
N
450
N
H
N
451
N
N
N
452
S
C
N
453
N
C
N
454
N
O
N
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
C
Y
459
N
N
Y
460
N
C
Y
461
N
C
Y
462
N
C
Y
463
N
C
Y
464
N
C
N
465
N
O
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
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
N
N
479
S
C
N
480
N
C
N
481
N
O
N
482
N
C
Y
483
N
C
Y
484
N
C
Y
485
N
C
Y
486
N
C
Y
487
N
C
Y
488
N
C
N
489
N
O
N
490
N
O
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
500
N
H
N
501
N
H
N
502
N
N
N
503
S
C
N
504
N
C
N
505
N
O
N
506
N
C
N
507
N
C
N
508
N
C
N
509
N
O
N
510
N
H
N
511
N
H
N
512
N
H
N
513
N
H
N
514
N
H
N
515
N
H
N
516
N
H
N
517
N
H
N
518
N
H
N
519
N
H
N
520
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
doub
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
doub
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
doub
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
doub
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
doub
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
sing
N
268
N
doub
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
Y
273
N
sing
Y
274
N
doub
Y
275
N
doub
N
276
N
sing
Y
277
N
sing
N
278
N
sing
Y
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
sing
N
290
N
sing
N
291
N
doub
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
doub
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
doub
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
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
doub
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
doub
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
Y
381
N
doub
Y
382
N
sing
Y
383
N
sing
N
384
N
sing
Y
385
N
doub
N
386
N
sing
Y
387
N
doub
N
388
N
sing
Y
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
sing
N
416
N
doub
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
N
444
N
sing
N
445
N
doub
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
Y
450
N
doub
Y
451
N
sing
Y
452
N
sing
N
453
N
sing
Y
454
N
doub
Y
455
N
sing
Y
456
N
sing
N
457
N
sing
Y
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
doub
N
474
N
sing
N
475
N
sing
N
476
N
sing
N
477
N
sing
Y
478
N
doub
Y
479
N
sing
Y
480
N
sing
N
481
N
sing
Y
482
N
doub
N
483
N
sing
Y
484
N
doub
N
485
N
sing
Y
486
N
sing
N
487
N
sing
N
488
N
sing
N
489
N
sing
N
490
N
sing
N
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
doub
N
498
N
sing
N
499
N
sing
N
500
N
sing
N
501
N
sing
N
502
N
sing
N
503
N
sing
N
504
N
sing
N
505
N
sing
N
506
N
sing
N
507
N
sing
N
508
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
356
967
981
10.1016/j.jmb.2005.11.094
16403521
Structural Insights into the Mechanisms of Drug Resistance in HIV-1 Protease NL4-3
2006
10.2210/pdb2azb/pdb
pdb_00002azb
100.0
1
MIRRORS
CCD
2005-04-21
MARMOSAIC 325 mm CCD
DOUBLE CRYSTAL MONOCHROMATOR
SINGLE WAVELENGTH
M
x-ray
1
0.979
1.0
BL9-2
SSRL
0.979
SYNCHROTRON
SSRL BEAMLINE BL9-2
10751.725
PROTEASE RETROPEPSIN
3.4.23.16
M46I,F53L,V82A
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
Half of TL-3 molecule in the asymmetric unit
1
syn
non-polymer
18.015
water
83
nat
water
HIV-1 PROTEASE
E.C.3.4.23.16
no
no
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKIIGGIGGLIKVRQYDQILIEICGHKAIGTVLVGPT
PANIIGRNLLTQIGCTLNF
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKIIGGIGGLIKVRQYDQILIEICGHKAIGTVLVGPT
PANIIGRNLLTQIGCTLNF
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
Lentivirus
R8
Escherichia
sample
Protease NL4-3
pol
11676
Human immunodeficiency virus 1
562
Escherichia coli
BL21.DE3, pLys S
plasmid
pET 21a+
1
2.10
41.00
8.50
PEG 4000, magensium chloride, Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281.16K, pH 8.50
281.16
pdbx_unobs_or_zero_occ_atoms
software
audit_author
citation_author
database_2
pdbx_unobs_or_zero_occ_atoms
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
Advisory
Refinement description
Database references
Structure summary
Advisory
Database references
Derived calculations
Data collection
Refinement description
1
0
2006-02-28
1
1
2008-05-01
1
2
2011-07-13
1
3
2013-02-27
1
4
2017-10-11
1
5
2018-01-24
1
6
2021-10-20
1
7
2023-08-23
_audit_author.name
_citation_author.name
_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
Wild-type protease NL4-3 in complex with same inhibitor, TL-3
1X protease NL4-3 in complex with the same inhibitor, TL-3
6X protease NL4-3 in complex with the same inhibitor, TL-3
N
RCSB
Y
RCSB
2005-09-09
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
HOH
water
THE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE.
THE STRUCTURE WAS REFINED WITH HALF OF THE C2 SYMMETRIC
LIGAND 3TL IN THE ASYMMETRIC UNIT - AS A RESULT A CLOSE
CONTACT SHOWS UP IN BETWEEN THE CARBON ATOMS CLOSEST TO
THE C2 SYMMETRY AXIS.
2AZ8
PDB ENTRY 2AZ8
PDB
experimental model
Inhibitor
N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide
Peptide-like
CBZ
200
2
3TL
3TL
200
A
HOH
1
3
HOH
HOH
100
A
HOH
2
3
HOH
HOH
101
A
HOH
3
3
HOH
HOH
102
A
HOH
4
3
HOH
HOH
103
A
HOH
5
3
HOH
HOH
104
A
HOH
6
3
HOH
HOH
105
A
HOH
7
3
HOH
HOH
106
A
HOH
8
3
HOH
HOH
107
A
HOH
9
3
HOH
HOH
108
A
HOH
10
3
HOH
HOH
109
A
HOH
11
3
HOH
HOH
110
A
HOH
12
3
HOH
HOH
111
A
HOH
13
3
HOH
HOH
112
A
HOH
14
3
HOH
HOH
113
A
HOH
15
3
HOH
HOH
114
A
HOH
16
3
HOH
HOH
115
A
HOH
17
3
HOH
HOH
116
A
HOH
18
3
HOH
HOH
117
A
HOH
19
3
HOH
HOH
118
A
HOH
20
3
HOH
HOH
119
A
HOH
21
3
HOH
HOH
120
A
HOH
22
3
HOH
HOH
121
A
HOH
23
3
HOH
HOH
122
A
HOH
24
3
HOH
HOH
123
A
HOH
25
3
HOH
HOH
124
A
HOH
26
3
HOH
HOH
125
A
HOH
27
3
HOH
HOH
126
A
HOH
28
3
HOH
HOH
127
A
HOH
29
3
HOH
HOH
128
A
HOH
30
3
HOH
HOH
129
A
HOH
31
3
HOH
HOH
130
A
HOH
32
3
HOH
HOH
131
A
HOH
33
3
HOH
HOH
132
A
HOH
34
3
HOH
HOH
133
A
HOH
35
3
HOH
HOH
134
A
HOH
36
3
HOH
HOH
135
A
HOH
37
3
HOH
HOH
136
A
HOH
38
3
HOH
HOH
137
A
HOH
39
3
HOH
HOH
138
A
HOH
40
3
HOH
HOH
139
A
HOH
41
3
HOH
HOH
140
A
HOH
42
3
HOH
HOH
141
A
HOH
43
3
HOH
HOH
142
A
HOH
44
3
HOH
HOH
143
A
HOH
45
3
HOH
HOH
144
A
HOH
46
3
HOH
HOH
145
A
HOH
47
3
HOH
HOH
146
A
HOH
48
3
HOH
HOH
147
A
HOH
49
3
HOH
HOH
148
A
HOH
50
3
HOH
HOH
149
A
HOH
51
3
HOH
HOH
150
A
HOH
52
3
HOH
HOH
151
A
HOH
53
3
HOH
HOH
152
A
HOH
55
3
HOH
HOH
153
A
HOH
56
3
HOH
HOH
154
A
HOH
57
3
HOH
HOH
155
A
HOH
58
3
HOH
HOH
156
A
HOH
59
3
HOH
HOH
157
A
HOH
60
3
HOH
HOH
158
A
HOH
61
3
HOH
HOH
159
A
HOH
62
3
HOH
HOH
160
A
HOH
63
3
HOH
HOH
161
A
HOH
64
3
HOH
HOH
162
A
HOH
65
3
HOH
HOH
163
A
HOH
66
3
HOH
HOH
164
A
HOH
67
3
HOH
HOH
165
A
HOH
68
3
HOH
HOH
166
A
HOH
69
3
HOH
HOH
167
A
HOH
70
3
HOH
HOH
168
A
HOH
71
3
HOH
HOH
169
A
HOH
72
3
HOH
HOH
170
A
HOH
73
3
HOH
HOH
171
A
HOH
74
3
HOH
HOH
172
A
HOH
75
3
HOH
HOH
173
A
HOH
76
3
HOH
HOH
174
A
HOH
77
3
HOH
HOH
175
A
HOH
78
3
HOH
HOH
176
A
HOH
79
3
HOH
HOH
177
A
HOH
81
3
HOH
HOH
178
A
HOH
82
3
HOH
HOH
179
A
HOH
83
3
HOH
HOH
180
A
HOH
84
3
HOH
HOH
181
A
HOH
85
3
HOH
HOH
182
A
0.394
0.594
3.000
3.000
24.370
24.370
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
ILE
46
n
46
ILE
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
n
52
52
A
n
53
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
ALA
82
n
82
ALA
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
author_and_software_defined_assembly
PISA
2
dimeric
5560
-18
9220
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
54.5680000000
A
N
LYS
45
A
N
LYS
45
A
O
VAL
56
A
O
VAL
56
A
N
ILE
64
A
N
ILE
64
A
O
ALA
71
A
O
ALA
71
A
O
LEU
76
A
O
LEU
76
A
N
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
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
1
A
CG
ASN
37
A
CG
ASN
37
0
Y
1
A
OD1
ASN
37
A
OD1
ASN
37
0
Y
1
A
ND2
ASN
37
A
ND2
ASN
37
0
Y
1
A
CB
ILE
46
A
CB
ILE
46
0
Y
1
A
CG1
ILE
46
A
CG1
ILE
46
0
Y
1
A
CG2
ILE
46
A
CG2
ILE
46
0
Y
1
A
CD1
ILE
46
A
CD1
ILE
46
0
Y
1
A
CG1
ILE
50
A
CG1
ILE
50
0
Y
1
A
CG2
ILE
50
A
CG2
ILE
50
0
Y
1
A
CD1
ILE
50
A
CD1
ILE
50
0
Y
1
A
CB
ILE
54
A
CB
ILE
54
0
Y
1
A
CG1
ILE
54
A
CG1
ILE
54
0
Y
1
A
CG2
ILE
54
A
CG2
ILE
54
0
Y
1
A
CD1
ILE
54
A
CD1
ILE
54
0
Y
1
A
CB
LYS
55
A
CB
LYS
55
0
Y
1
A
CG
LYS
55
A
CG
LYS
55
0
Y
1
A
CD
LYS
55
A
CD
LYS
55
0
Y
1
A
CE
LYS
55
A
CE
LYS
55
0
Y
1
A
NZ
LYS
55
A
NZ
LYS
55
0
Y
1
A
N51
3TL
200
B
N51
3TL
1
1
N
1
A
C51
3TL
200
B
C51
3TL
1
1
N
1
A
C52
3TL
200
B
C52
3TL
1
1
N
1
A
O51
3TL
200
B
O51
3TL
1
1
N
1
A
C53
3TL
200
B
C53
3TL
1
1
N
1
A
C54
3TL
200
B
C54
3TL
1
1
N
1
A
C55
3TL
200
B
C55
3TL
1
1
N
1
A
C59
3TL
200
B
C59
3TL
1
1
N
1
A
C56
3TL
200
B
C56
3TL
1
1
N
1
A
C58
3TL
200
B
C58
3TL
1
1
N
1
A
C57
3TL
200
B
C57
3TL
1
1
N
1
A
N52
3TL
200
B
N52
3TL
1
1
N
1
A
C60
3TL
200
B
C60
3TL
1
1
N
1
A
C61
3TL
200
B
C61
3TL
1
1
N
1
A
O52
3TL
200
B
O52
3TL
1
1
N
1
A
C62
3TL
200
B
C62
3TL
1
1
N
1
A
CG6
3TL
200
B
CG6
3TL
1
1
N
1
A
CG5
3TL
200
B
CG5
3TL
1
1
N
1
A
N54
3TL
200
B
N54
3TL
1
1
N
1
A
C68
3TL
200
B
C68
3TL
1
1
N
1
A
C69
3TL
200
B
C69
3TL
1
1
N
1
A
O54
3TL
200
B
O54
3TL
1
1
N
1
A
C70
3TL
200
B
C70
3TL
1
1
N
1
A
C81
3TL
200
B
C81
3TL
1
1
N
1
A
O58
3TL
200
B
O58
3TL
1
1
N
1
A
O59
3TL
200
B
O59
3TL
1
1
N
1
A
CA5
3TL
200
B
CA5
3TL
1
1
N
1
A
C50
3TL
200
B
C50
3TL
1
1
N
1
A
C63
3TL
200
B
C63
3TL
1
1
N
1
A
C64
3TL
200
B
C64
3TL
1
1
N
1
A
C65
3TL
200
B
C65
3TL
1
1
N
1
A
C66
3TL
200
B
C66
3TL
1
1
N
1
A
C67
3TL
200
B
C67
3TL
1
1
N
1
A
GLY
52
A
GLY
52
1
Y
1
A
LEU
53
A
LEU
53
1
Y
1
A
A
C2
C2
3TL
3TL
200
200
1.46
1_555
9_555
1
A
ILE
50
-93.43
-62.56
38.46
0.287
0.219
0.219
2.03
24.40
346
6841
6816
5.000
99.6
RANDOM
1
THROUGHOUT
2.000
MOLECULAR REPLACEMENT
PDB ENTRY 2AZ8
ENGH & HUBER
2.03
24.40
83
859
33
0
743
0.017
1.80
25.50
1.24
2.030
24.400
2AZB
6816
1.000
0.064
1
24.3000
14.300
99.6
0.199
2.03
2.18
4.100
1
13.50
100.0
data collection
MAR345
data reduction
MOSFLM
phasing
MOLREP
refinement
CNS
HIV-1 Protease NL4-3 3X mutant in complex with inhibitor, TL-3
1
N
N
2
N
N
3
N
N
The second monomer of the biological dimer is generated by the two fold axis: Y,X,-Z+1/3
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
HYDROLASE/HYDROLASE INHIBITOR
HIV-1, protease, inhibitor, TL-3, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
POL_HV1BR
UNP
1
69
P03367
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
69
167
2AZB
1
99
P03367
A
1
1
99
1
GLN
variant
LYS
7
2AZB
A
P03367
UNP
75
7
1
SER
variant
ASN
37
2AZB
A
P03367
UNP
105
37
1
MET
engineered mutation
ILE
46
2AZB
A
P03367
UNP
114
46
1
PHE
engineered mutation
LEU
53
2AZB
A
P03367
UNP
121
53
1
VAL
engineered mutation
ALA
82
2AZB
A
P03367
UNP
150
82
8
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
LYS
43
A
LYS
43
A
ILE
46
A
ILE
46
A
LYS
55
A
LYS
55
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
LYS
55
A
LYS
55
A
ILE
66
A
ILE
66
BINDING SITE FOR RESIDUE 3TL A 200
A
3TL
200
Software
16
A
ARG
8
A
ARG
8
16
9_555
A
ASP
25
A
ASP
25
16
9_555
A
ASP
25
A
ASP
25
16
1_555
A
GLY
27
A
GLY
27
16
1_555
A
ALA
28
A
ALA
28
16
1_555
A
ASP
29
A
ASP
29
16
1_555
A
ASP
30
A
ASP
30
16
1_555
A
ILE
47
A
ILE
47
16
1_555
A
GLY
48
A
GLY
48
16
1_555
A
GLY
49
A
GLY
49
16
1_555
A
GLY
49
A
GLY
49
16
11_455
A
ILE
50
A
ILE
50
16
1_555
A
PRO
81
A
PRO
81
16
9_555
A
ILE
84
A
ILE
84
16
9_555
A
HOH
171
C
HOH
16
1_555
A
HOH
182
C
HOH
16
1_555
178
P 61 2 2