0.019871
0.011473
0.000000
0.000000
0.022945
0.000000
0.000000
0.000000
0.013484
0.00000
0.00000
0.00000
Heaslet, H.
Lin, Y.C.
Elder, J.H.
Stout, C.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
50.324
50.324
74.161
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
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
C
Y
460
N
C
Y
461
N
C
N
462
N
O
N
463
N
O
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
N
N
476
S
C
N
477
N
C
N
478
N
O
N
479
N
C
N
480
N
C
N
481
N
C
N
482
N
O
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
H
N
493
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
N
455
N
sing
Y
456
N
doub
N
457
N
sing
Y
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
doub
N
470
N
sing
N
471
N
sing
N
472
N
sing
N
473
N
sing
N
474
N
sing
N
475
N
sing
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
UK
Retrovirology
1742-4690
4
1
1
10.1186/1742-4690-4-1
17212810
Crystal structure of an FIV/HIV chimeric protease complexed with the broad-based inhibitor, TL-3.
2007
10.2210/pdb2hah/pdb
pdb_00002hah
100
1
Double-crystal monochromator, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing
CCD
2006-02-18
ADSC QUANTUM 315
Double crystal, parallel
SINGLE WAVELENGTH
M
x-ray
1
0.97944
1.0
BL1-5
SSRL
0.97944
SYNCHROTRON
SSRL BEAMLINE BL1-5
13226.226
Protease
3.4.23.16
residues 39-154
I37V, N55M, M56I, I57G, V59I, G62F, K63I, L97T, I98P, Q99V, P100N, L101I
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
18.015
water
120
nat
water
Retropepsin
no
no
YNKVGTTTTLEKRPEILIFVNGYPIKFLLDTGADITVLNRRDFQVKNSIENGRQMIGGIGGFIRGTNYINVHLEIRDENY
KTQCIFGNVCVLEDNSTPVNILGRDNMIKFNIRLVM
YNKVGTTTTLEKRPEILIFVNGYPIKFLLDTGADITVLNRRDFQVKNSIENGRQMIGGIGGFIRGTNYINVHLEIRDENY
KTQCIFGNVCVLEDNSTPVNILGRDNMIKFNIRLVM
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Lentivirus
Feline immunodeficiency virus
isolate petaluma
Escherichia
sample
POL
11674
Feline immunodeficiency virus (isolate Petaluma)
562
Escherichia coli
Rosetta(DE3)pLysS
plasmid
pET-21a(+)
1
2.05
39.97
VAPOR DIFFUSION, HANGING DROP
7.5
100mM Hepes, 2.5M LiCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281.16K
281.16
database_2
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
Database references
Derived calculations
Data collection
Refinement description
1
0
2007-02-13
1
1
2008-05-01
1
2
2011-07-13
1
3
2013-02-27
1
4
2021-10-20
1
5
2023-08-30
_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
Structure of wild-type FIV protease in complex with TL-3
Structure of wild-type HIV protease in complex with TL-3
RCSB
Y
RCSB
2006-06-12
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
5FIV
pdb entry 5FIV
PDB
experimental model
Inhibitor
N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide
Peptide-like
3TL
201
2
3TL
3TL
201
A
HOH
202
3
HOH
HOH
202
A
HOH
203
3
HOH
HOH
203
A
HOH
204
3
HOH
HOH
204
A
HOH
205
3
HOH
HOH
205
A
HOH
206
3
HOH
HOH
206
A
HOH
207
3
HOH
HOH
207
A
HOH
208
3
HOH
HOH
208
A
HOH
209
3
HOH
HOH
209
A
HOH
210
3
HOH
HOH
210
A
HOH
211
3
HOH
HOH
211
A
HOH
212
3
HOH
HOH
212
A
HOH
213
3
HOH
HOH
213
A
HOH
214
3
HOH
HOH
214
A
HOH
215
3
HOH
HOH
215
A
HOH
216
3
HOH
HOH
216
A
HOH
217
3
HOH
HOH
217
A
HOH
218
3
HOH
HOH
218
A
HOH
219
3
HOH
HOH
219
A
HOH
220
3
HOH
HOH
220
A
HOH
221
3
HOH
HOH
221
A
HOH
222
3
HOH
HOH
222
A
HOH
223
3
HOH
HOH
223
A
HOH
224
3
HOH
HOH
224
A
HOH
225
3
HOH
HOH
225
A
HOH
226
3
HOH
HOH
226
A
HOH
227
3
HOH
HOH
227
A
HOH
228
3
HOH
HOH
228
A
HOH
229
3
HOH
HOH
229
A
HOH
230
3
HOH
HOH
230
A
HOH
231
3
HOH
HOH
231
A
HOH
232
3
HOH
HOH
232
A
HOH
233
3
HOH
HOH
233
A
HOH
234
3
HOH
HOH
234
A
HOH
235
3
HOH
HOH
235
A
HOH
236
3
HOH
HOH
236
A
HOH
237
3
HOH
HOH
237
A
HOH
238
3
HOH
HOH
238
A
HOH
239
3
HOH
HOH
239
A
HOH
240
3
HOH
HOH
240
A
HOH
241
3
HOH
HOH
241
A
HOH
242
3
HOH
HOH
242
A
HOH
243
3
HOH
HOH
243
A
HOH
244
3
HOH
HOH
244
A
HOH
245
3
HOH
HOH
245
A
HOH
246
3
HOH
HOH
246
A
HOH
247
3
HOH
HOH
247
A
HOH
248
3
HOH
HOH
248
A
HOH
249
3
HOH
HOH
249
A
HOH
250
3
HOH
HOH
250
A
HOH
251
3
HOH
HOH
251
A
HOH
252
3
HOH
HOH
252
A
HOH
253
3
HOH
HOH
253
A
HOH
254
3
HOH
HOH
254
A
HOH
255
3
HOH
HOH
255
A
HOH
256
3
HOH
HOH
256
A
HOH
257
3
HOH
HOH
257
A
HOH
258
3
HOH
HOH
258
A
HOH
259
3
HOH
HOH
259
A
HOH
260
3
HOH
HOH
260
A
HOH
261
3
HOH
HOH
261
A
HOH
262
3
HOH
HOH
262
A
HOH
263
3
HOH
HOH
263
A
HOH
264
3
HOH
HOH
264
A
HOH
265
3
HOH
HOH
265
A
HOH
266
3
HOH
HOH
266
A
HOH
267
3
HOH
HOH
267
A
HOH
268
3
HOH
HOH
268
A
HOH
269
3
HOH
HOH
269
A
HOH
270
3
HOH
HOH
270
A
HOH
271
3
HOH
HOH
271
A
HOH
272
3
HOH
HOH
272
A
HOH
273
3
HOH
HOH
273
A
HOH
274
3
HOH
HOH
274
A
HOH
275
3
HOH
HOH
275
A
HOH
276
3
HOH
HOH
276
A
HOH
277
3
HOH
HOH
277
A
HOH
278
3
HOH
HOH
278
A
HOH
279
3
HOH
HOH
279
A
HOH
280
3
HOH
HOH
280
A
HOH
281
3
HOH
HOH
281
A
HOH
282
3
HOH
HOH
282
A
HOH
283
3
HOH
HOH
283
A
HOH
284
3
HOH
HOH
284
A
HOH
285
3
HOH
HOH
285
A
HOH
286
3
HOH
HOH
286
A
HOH
287
3
HOH
HOH
287
A
HOH
288
3
HOH
HOH
288
A
HOH
289
3
HOH
HOH
289
A
HOH
290
3
HOH
HOH
290
A
HOH
291
3
HOH
HOH
291
A
HOH
292
3
HOH
HOH
292
A
HOH
293
3
HOH
HOH
293
A
HOH
294
3
HOH
HOH
294
A
HOH
295
3
HOH
HOH
295
A
HOH
296
3
HOH
HOH
296
A
HOH
297
3
HOH
HOH
297
A
HOH
298
3
HOH
HOH
298
A
HOH
299
3
HOH
HOH
299
A
HOH
300
3
HOH
HOH
300
A
HOH
301
3
HOH
HOH
301
A
HOH
302
3
HOH
HOH
302
A
HOH
303
3
HOH
HOH
303
A
HOH
304
3
HOH
HOH
304
A
HOH
305
3
HOH
HOH
305
A
HOH
306
3
HOH
HOH
306
A
HOH
307
3
HOH
HOH
307
A
HOH
308
3
HOH
HOH
308
A
HOH
309
3
HOH
HOH
309
A
HOH
310
3
HOH
HOH
310
A
HOH
311
3
HOH
HOH
311
A
HOH
312
3
HOH
HOH
312
A
HOH
313
3
HOH
HOH
313
A
HOH
314
3
HOH
HOH
314
A
HOH
315
3
HOH
HOH
315
A
HOH
316
3
HOH
HOH
316
A
HOH
317
3
HOH
HOH
317
A
HOH
318
3
HOH
HOH
318
A
HOH
319
3
HOH
HOH
319
A
HOH
320
3
HOH
HOH
320
A
HOH
321
3
HOH
HOH
321
A
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
GLY
5
n
5
GLY
5
A
THR
6
n
6
THR
6
A
THR
7
n
7
THR
7
A
THR
8
n
8
THR
8
A
THR
9
n
9
THR
9
A
LEU
10
n
10
LEU
10
A
GLU
11
n
11
GLU
11
A
LYS
12
n
12
LYS
12
A
ARG
13
n
13
ARG
13
A
PRO
14
n
14
PRO
14
A
GLU
15
n
15
GLU
15
A
ILE
16
n
16
ILE
16
A
LEU
17
n
17
LEU
17
A
ILE
18
n
18
ILE
18
A
PHE
19
n
19
PHE
19
A
VAL
20
n
20
VAL
20
A
ASN
21
n
21
ASN
21
A
GLY
22
n
22
GLY
22
A
TYR
23
n
23
TYR
23
A
PRO
24
n
24
PRO
24
A
ILE
25
n
25
ILE
25
A
LYS
26
n
26
LYS
26
A
PHE
27
n
27
PHE
27
A
LEU
28
n
28
LEU
28
A
LEU
29
n
29
LEU
29
A
ASP
30
n
30
ASP
30
A
THR
31
n
31
THR
31
A
GLY
32
n
32
GLY
32
A
ALA
33
n
33
ALA
33
A
ASP
34
n
34
ASP
34
A
ILE
35
n
35
ILE
35
A
THR
36
n
36
THR
36
A
VAL
37
n
37
VAL
37
A
LEU
38
n
38
LEU
38
A
ASN
39
n
39
ASN
39
A
ARG
40
n
40
ARG
40
A
ARG
41
n
41
ARG
41
A
ASP
42
n
42
ASP
42
A
PHE
43
n
43
PHE
43
A
GLN
44
n
44
GLN
44
A
VAL
45
n
45
VAL
45
A
LYS
46
n
46
LYS
46
A
ASN
47
n
47
ASN
47
A
SER
48
n
48
SER
48
A
ILE
49
n
49
ILE
49
A
GLU
50
n
50
GLU
50
A
ASN
51
n
51
ASN
51
A
GLY
52
n
52
GLY
52
A
ARG
53
n
53
ARG
53
A
GLN
54
n
54
GLN
54
A
MET
55
n
55
MET
55
A
ILE
56
n
56
ILE
56
A
GLY
57
n
57
GLY
57
A
GLY
58
n
58
GLY
58
A
ILE
59
n
59
ILE
59
A
GLY
60
n
60
GLY
60
A
GLY
61
n
61
GLY
61
A
PHE
62
n
62
PHE
62
A
ILE
63
n
63
ILE
63
A
ARG
64
n
64
ARG
64
A
GLY
65
n
65
GLY
65
A
THR
66
n
66
THR
66
A
ASN
67
n
67
ASN
67
A
TYR
68
n
68
TYR
68
A
ILE
69
n
69
ILE
69
A
ASN
70
n
70
ASN
70
A
VAL
71
n
71
VAL
71
A
HIS
72
n
72
HIS
72
A
LEU
73
n
73
LEU
73
A
GLU
74
n
74
GLU
74
A
ILE
75
n
75
ILE
75
A
ARG
76
n
76
ARG
76
A
ASP
77
n
77
ASP
77
A
GLU
78
n
78
GLU
78
A
ASN
79
n
79
ASN
79
A
TYR
80
n
80
TYR
80
A
LYS
81
n
81
LYS
81
A
THR
82
n
82
THR
82
A
GLN
83
n
83
GLN
83
A
CYS
84
n
84
CYS
84
A
ILE
85
n
85
ILE
85
A
PHE
86
n
86
PHE
86
A
GLY
87
n
87
GLY
87
A
ASN
88
n
88
ASN
88
A
VAL
89
n
89
VAL
89
A
CYS
90
n
90
CYS
90
A
VAL
91
n
91
VAL
91
A
LEU
92
n
92
LEU
92
A
GLU
93
n
93
GLU
93
A
ASP
94
n
94
ASP
94
A
ASN
95
n
95
ASN
95
A
SER
96
n
96
SER
96
A
THR
97
n
97
THR
97
A
PRO
98
n
98
PRO
98
A
VAL
99
n
99
VAL
99
A
ASN
100
n
100
ASN
100
A
ILE
101
n
101
ILE
101
A
LEU
102
n
102
LEU
102
A
GLY
103
n
103
GLY
103
A
ARG
104
n
104
ARG
104
A
ASP
105
n
105
ASP
105
A
ASN
106
n
106
ASN
106
A
MET
107
n
107
MET
107
A
ILE
108
n
108
ILE
108
A
LYS
109
n
109
LYS
109
A
PHE
110
n
110
PHE
110
A
ASN
111
n
111
ASN
111
A
ILE
112
n
112
ILE
112
A
ARG
113
n
113
ARG
113
A
LEU
114
n
114
LEU
114
A
VAL
115
n
115
VAL
115
A
MET
116
n
116
MET
116
A
author_and_software_defined_assembly
PISA,PQS
2
dimeric
5450
-22
10220
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
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
5_553
x-y,-y,-z-4/3
crystal symmetry operation
0.0000000000
0.0000000000
-98.8813333333
A
N
ILE
49
A
N
ILE
49
A
O
ILE
69
A
O
ILE
69
A
N
THR
66
A
N
THR
66
A
O
VAL
91
A
O
VAL
91
A
O
LEU
92
A
O
LEU
92
A
N
LEU
38
A
N
LEU
38
A
N
VAL
37
A
N
VAL
37
A
O
ILE
101
A
O
ILE
101
A
O
LEU
102
A
O
LEU
102
A
N
LEU
28
A
N
LEU
28
A
O
TYR
23
A
O
TYR
23
A
N
VAL
20
A
N
VAL
20
A
N
PHE
19
A
N
PHE
19
A
O
GLU
74
A
O
GLU
74
1
A
HOH
231
C
HOH
1
A
CD
LYS
81
A
CD
LYS
81
0
Y
1
A
CE
LYS
81
A
CE
LYS
81
0
Y
1
A
NZ
LYS
81
A
NZ
LYS
81
0
Y
1
A
N51
3TL
201
B
N51
3TL
1
1
N
1
A
C51
3TL
201
B
C51
3TL
1
1
N
1
A
C52
3TL
201
B
C52
3TL
1
1
N
1
A
O51
3TL
201
B
O51
3TL
1
1
N
1
A
C53
3TL
201
B
C53
3TL
1
1
N
1
A
C54
3TL
201
B
C54
3TL
1
1
N
1
A
C55
3TL
201
B
C55
3TL
1
1
N
1
A
C59
3TL
201
B
C59
3TL
1
1
N
1
A
C56
3TL
201
B
C56
3TL
1
1
N
1
A
C58
3TL
201
B
C58
3TL
1
1
N
1
A
C57
3TL
201
B
C57
3TL
1
1
N
1
A
N52
3TL
201
B
N52
3TL
1
1
N
1
A
C60
3TL
201
B
C60
3TL
1
1
N
1
A
C61
3TL
201
B
C61
3TL
1
1
N
1
A
O52
3TL
201
B
O52
3TL
1
1
N
1
A
C62
3TL
201
B
C62
3TL
1
1
N
1
A
CG6
3TL
201
B
CG6
3TL
1
1
N
1
A
CG5
3TL
201
B
CG5
3TL
1
1
N
1
A
N54
3TL
201
B
N54
3TL
1
1
N
1
A
C68
3TL
201
B
C68
3TL
1
1
N
1
A
C69
3TL
201
B
C69
3TL
1
1
N
1
A
O54
3TL
201
B
O54
3TL
1
1
N
1
A
C70
3TL
201
B
C70
3TL
1
1
N
1
A
C81
3TL
201
B
C81
3TL
1
1
N
1
A
O58
3TL
201
B
O58
3TL
1
1
N
1
A
O59
3TL
201
B
O59
3TL
1
1
N
1
A
CA5
3TL
201
B
CA5
3TL
1
1
N
1
A
C50
3TL
201
B
C50
3TL
1
1
N
1
A
C63
3TL
201
B
C63
3TL
1
1
N
1
A
C64
3TL
201
B
C64
3TL
1
1
N
1
A
C65
3TL
201
B
C65
3TL
1
1
N
1
A
C66
3TL
201
B
C66
3TL
1
1
N
1
A
C67
3TL
201
B
C67
3TL
1
1
N
1
A
TYR
1
A
TYR
1
1
Y
1
A
ASN
2
A
ASN
2
1
Y
1
A
LYS
3
A
LYS
3
1
Y
1
A
VAL
4
A
VAL
4
1
Y
1
A
LYS
46
52.24
-126.33
1
A
ASN
51
-146.35
39.49
protein_rep.param
int.par
water_rep.param
24.431
0.375
0.610
0.000
0.375
0.000
-0.751
0.233
0.184
0.184
0.233
1.700
74.000
627
12424
12396
5.000
99.600
0.874
Random
1
0.00
MOLECULAR REPLACEMENT
pdb entry 5FIV
Engh & Huber
60.962
1.700
74.000
120
1045
33
0
892
1.166
1.500
2.112
2.000
1.772
2.000
3.055
2.500
0.265
0.251
1.750
56
960
1016
12
0.257
0.231
1.810
41
967
1008
12
0.335
0.221
1.870
49
972
1021
12
0.269
0.228
1.950
61
954
1015
12
0.245
0.186
2.030
44
975
1019
12
0.204
0.182
2.140
48
970
1018
12
0.241
0.18
2.280
50
983
1033
12
0.261
0.2
2.450
45
976
1021
12
0.218
0.16
2.700
60
968
1028
12
0.241
0.193
3.090
59
1004
1063
12
0.21
0.162
3.890
61
999
1060
12
0.22
0.175
74.000
53
1041
1094
12
1.7
74.0
2HAH
12484
12440
2.0
3.0
0.07
1
6.2
97.0
0.368
1.7
2.6
5451
1
6.0
99.0
data scaling
Pflugrath, J.W.
jwp@RigakuMSC.com
http://www.msc.com/protein/dtrek.html
d*TREK
package
phasing
A. Vagin
alexei@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/molrep.html
MOLREP
other
refinement
Axel T. Brunger
axel.brunger@yale.edu
Fortran_77
http://cns.csb.yale.edu/v1.1/
CNS
package
data extraction
PDB
sw-help@rcsb.rutgers.edu
April. 3, 2006
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
2.000
data collection
Blu-Ice
data reduction
MOSFLM
The structure of FIV 12S protease in complex with TL-3
1
N
N
2
N
N
3
N
N
A
ARG
41
A
ARG
41
HELX_P
A
PHE
43
A
PHE
43
5
1
3
A
GLY
103
A
GLY
103
HELX_P
A
ILE
108
A
ILE
108
1
2
6
HYDROLASE/HYDROLASE INHIBITOR
retroviral, protease, aspartyl, feline, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
POL_FIVPE
UNP
1
39
P16088
YNKVGTTTTLEKRPEILIFVNGYPIKFLLDTGADITILNRRDFQVKNSIENGRQNMIGVGGGKRGTNYINVHLEIRDENY
KTQCIFGNVCVLEDNSLIQPLLGRDNMIKFNIRLVM
39
154
2HAH
1
116
P16088
A
1
1
116
1
ILE
engineered mutation
VAL
37
2HAH
A
P16088
UNP
75
37
1
ASN
engineered mutation
MET
55
2HAH
A
P16088
UNP
93
55
1
MET
engineered mutation
ILE
56
2HAH
A
P16088
UNP
94
56
1
ILE
engineered mutation
GLY
57
2HAH
A
P16088
UNP
95
57
1
VAL
engineered mutation
ILE
59
2HAH
A
P16088
UNP
97
59
1
GLY
engineered mutation
PHE
62
2HAH
A
P16088
UNP
100
62
1
LYS
engineered mutation
ILE
63
2HAH
A
P16088
UNP
101
63
1
LEU
engineered mutation
THR
97
2HAH
A
P16088
UNP
135
97
1
ILE
engineered mutation
PRO
98
2HAH
A
P16088
UNP
136
98
1
GLN
engineered mutation
VAL
99
2HAH
A
P16088
UNP
137
99
1
PRO
engineered mutation
ASN
100
2HAH
A
P16088
UNP
138
100
1
LEU
engineered mutation
ILE
101
2HAH
A
P16088
UNP
139
101
8
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
ILE
49
A
ILE
49
A
GLY
58
A
GLY
58
A
GLY
61
A
GLY
61
A
ILE
75
A
ILE
75
A
GLN
83
A
GLN
83
A
LEU
92
A
LEU
92
A
VAL
37
A
VAL
37
A
ASN
39
A
ASN
39
A
ASN
100
A
ASN
100
A
LEU
102
A
LEU
102
A
TYR
23
A
TYR
23
A
LEU
29
A
LEU
29
A
GLU
15
A
GLU
15
A
VAL
20
A
VAL
20
A
GLY
61
A
GLY
61
A
ILE
75
A
ILE
75
BINDING SITE FOR RESIDUE 3TL A 201
A
3TL
201
Software
19
A
ARG
13
A
ARG
13
19
5_553
A
PRO
24
A
PRO
24
19
2_655
A
ILE
25
A
ILE
25
19
2_655
A
ASP
30
A
ASP
30
19
1_555
A
ASP
30
A
ASP
30
19
5_553
A
GLY
32
A
GLY
32
19
1_555
A
ALA
33
A
ALA
33
19
1_555
A
ASP
34
A
ASP
34
19
1_555
A
GLN
54
A
GLN
54
19
1_555
A
MET
55
A
MET
55
19
1_555
A
ILE
56
A
ILE
56
19
1_555
A
GLY
57
A
GLY
57
19
1_555
A
GLY
58
A
GLY
58
19
1_555
A
ILE
59
A
ILE
59
19
1_555
A
ILE
59
A
ILE
59
19
5_553
A
PRO
98
A
PRO
98
19
5_553
A
VAL
99
A
VAL
99
19
5_553
A
HOH
231
C
HOH
19
5_553
A
HOH
231
C
HOH
19
1_555
152
P 31 2 1