0.019428
0.000000
0.000000
0.000000
0.017157
0.000000
0.000000
0.000000
0.016273
0.000000
0.000000
0.000000
Torbeev, V.Y.
Kent, S.B.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
90.000
90.000
51.472
58.286
61.450
C35 H68 N11 O8 1
770.983
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
p2/NC
peptide-like
C4 H9 N O2
103.120
n
ALPHA-AMINOBUTYRIC ACID
L-peptide linking
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
89.093
D-ALANINE
D-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
C6 H13 N O2
131.173
n
NORLEUCINE
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
C5 H10 N2 O3 S
178.209
n
S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
CYSTEINE-S-ACETAMIDE
L-peptide linking
N
1
N
C
N
2
N
O
N
3
N
C
N
4
N
N
N
5
S
C
N
6
N
C
N
7
N
O
N
8
R
C
N
9
N
O
N
10
N
C
N
11
N
N
N
12
S
C
N
13
N
C
N
14
N
O
N
15
S
C
N
16
N
C
N
17
N
C
N
18
N
C
N
19
N
N
N
20
S
C
N
21
N
C
N
22
N
C
N
23
N
C
N
24
N
C
N
25
N
C
N
26
N
N
N
27
S
C
N
28
N
C
N
29
N
O
N
30
N
C
N
31
N
C
N
32
N
C
N
33
N
C
N
34
N
N
N
35
S
C
N
36
N
C
N
37
N
O
N
38
N
C
N
39
N
C
N
40
N
C
N
41
N
O
N
42
N
N
N
43
N
N
N
44
S
C
N
45
N
C
N
46
N
O
N
47
N
C
N
48
N
C
N
49
N
C
N
50
N
N
N
51
N
C
N
52
N
N
N
53
N
N
N
54
N
N
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
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
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
N
129
N
O
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
N
N
140
S
C
N
141
N
C
N
142
N
O
N
143
N
C
N
144
N
O
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
N
N
153
S
C
N
154
N
C
N
155
N
O
N
156
N
C
N
157
N
C
N
158
N
C
N
159
N
N
N
160
N
C
N
161
N
N
N
162
N
N
N
163
N
O
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
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
N
N
180
S
C
N
181
N
C
N
182
N
O
N
183
N
C
N
184
N
C
N
185
N
O
N
186
N
N
N
187
N
O
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
N
N
197
S
C
N
198
N
C
N
199
N
O
N
200
N
C
N
201
N
C
N
202
N
O
N
203
N
O
N
204
N
O
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
N
N
213
R
C
N
214
N
C
N
215
N
C
N
216
N
O
N
217
N
O
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
N
N
226
S
C
N
227
N
C
N
228
N
O
N
229
N
C
N
230
N
C
N
231
N
C
N
232
N
O
N
233
N
N
N
234
N
O
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
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
N
N
246
S
C
N
247
N
C
N
248
N
O
N
249
N
C
N
250
N
C
N
251
N
C
N
252
N
O
N
253
N
O
N
254
N
O
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
N
N
265
N
C
N
266
N
C
N
267
N
O
N
268
N
O
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
N
C
Y
279
N
C
Y
280
N
N
Y
281
N
C
Y
282
N
C
Y
283
N
N
N
284
N
O
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
O
N
296
N
H
N
297
N
H
N
298
N
N
N
299
S
C
N
300
N
C
N
301
N
O
N
302
S
C
N
303
N
C
N
304
N
C
N
305
N
C
N
306
N
O
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
H
N
320
N
N
N
321
S
C
N
322
N
C
N
323
N
O
N
324
N
C
N
325
N
C
N
326
N
C
N
327
N
C
N
328
N
O
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
N
N
343
S
C
N
344
N
C
N
345
N
O
N
346
N
C
N
347
N
C
N
348
N
C
N
349
N
C
N
350
N
N
N
351
N
O
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
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
O
N
372
N
C
N
373
N
C
N
374
N
C
N
375
N
C
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
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
N
N
390
S
C
N
391
N
C
N
392
N
O
N
393
N
C
Y
394
N
C
Y
395
N
C
Y
396
N
C
Y
397
N
C
Y
398
N
C
Y
399
N
C
N
400
N
O
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
N
N
413
S
C
N
414
N
C
N
415
N
O
N
416
N
C
N
417
N
C
N
418
N
C
N
419
N
O
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
N
N
430
S
C
N
431
N
C
N
432
N
O
N
433
R
C
N
434
N
O
N
435
N
C
N
436
N
O
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
N
N
447
S
C
N
448
N
C
N
449
N
O
N
450
N
C
Y
451
N
C
Y
452
N
C
Y
453
N
C
Y
454
N
N
Y
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
C
Y
459
N
C
N
460
N
O
N
461
N
H
N
462
N
H
N
463
N
H
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
N
N
474
S
C
N
475
N
C
N
476
N
O
N
477
N
C
Y
478
N
C
Y
479
N
C
Y
480
N
C
Y
481
N
C
Y
482
N
C
Y
483
N
C
N
484
N
O
N
485
N
O
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
494
N
H
N
495
N
H
N
496
N
H
N
497
N
N
N
498
S
C
N
499
N
C
N
500
N
O
N
501
N
C
N
502
N
C
N
503
N
C
N
504
N
O
N
505
N
H
N
506
N
H
N
507
N
H
N
508
N
H
N
509
N
H
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
N
N
517
R
C
N
518
N
C
N
519
N
S
N
520
N
C
N
521
N
C
N
522
N
O
N
523
N
N
N
524
N
C
N
525
N
O
N
526
N
O
N
527
N
H
N
528
N
H
N
529
N
H
N
530
N
H
N
531
N
H
N
532
N
H
N
533
N
H
N
534
N
H
N
535
N
H
N
536
N
H
N
1
N
doub
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
doub
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
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
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
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
N
57
N
sing
N
58
N
sing
N
59
N
doub
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
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
doub
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
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
doub
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
doub
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
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
doub
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
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
doub
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
sing
N
153
N
sing
N
154
N
sing
N
155
N
doub
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
sing
N
167
N
sing
N
168
N
sing
N
169
N
doub
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
doub
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
doub
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
doub
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
doub
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
doub
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
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
doub
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
sing
N
260
N
sing
N
261
N
doub
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
sing
N
269
N
sing
N
270
N
doub
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
Y
275
N
sing
Y
276
N
doub
Y
277
N
doub
N
278
N
sing
Y
279
N
sing
N
280
N
sing
Y
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
sing
N
292
N
sing
N
293
N
doub
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
sing
N
314
N
doub
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
doub
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
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
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
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
doub
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
Y
385
N
doub
Y
386
N
sing
Y
387
N
sing
N
388
N
sing
Y
389
N
doub
N
390
N
sing
Y
391
N
doub
N
392
N
sing
Y
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
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
doub
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
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
doub
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
sing
N
435
N
sing
N
436
N
doub
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
Y
441
N
doub
Y
442
N
sing
Y
443
N
sing
N
444
N
sing
Y
445
N
doub
Y
446
N
sing
Y
447
N
sing
N
448
N
sing
Y
449
N
sing
Y
450
N
doub
N
451
N
sing
Y
452
N
doub
N
453
N
sing
Y
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
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
doub
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
Y
469
N
doub
Y
470
N
sing
Y
471
N
sing
N
472
N
sing
Y
473
N
doub
N
474
N
sing
Y
475
N
doub
N
476
N
sing
Y
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
sing
N
486
N
sing
N
487
N
sing
N
488
N
doub
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
sing
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
N
509
N
sing
N
510
N
sing
N
511
N
sing
N
512
N
sing
N
513
N
doub
N
514
N
sing
N
515
N
sing
N
516
N
sing
N
517
N
doub
N
518
N
sing
N
519
N
sing
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
108
20982
20987
10.1073/pnas.1111202108
22158985
Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.
2011
10.2210/pdb3fsm/pdb
pdb_00003fsm
110
1
double crystal monochromator and K-B pair of biomorph mirrors for vertical and
horizontal focusing with two additional horizontally deflecting mirrors
CCD
2007-02-26
MARMOSAIC 300 mm CCD
double crystal monochromator
SINGLE WAVELENGTH
M
x-ray
1
1.03320
1.0
23-ID-B
APS
1.03320
SYNCHROTRON
APS BEAMLINE 23-ID-B
21919.703
COVALENT DIMER [L-Ala51, D-Ala51'] HIV-1 PROTEASE
3.4.23.16
1
syn
polymer
Total chemical peptide synthesis
770.983
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
1
syn
non-polymer
18.015
water
118
nat
water
no
yes
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEE(NLE)NLPG(YCM)WKPK(NLE)IGGIAGFIKVRQYDQIPVEI
(ABA)GHKAIGTVLVGPTPVNIIGRNLLTQIG(ABA)TLNF(YCM)GGGGPQITLWKRPLVTIRIGGQLKEALLDTGADD
TVIEE(NLE)NLPG(YCM)WKPK(NLE)IGGI(DAL)GFIKVRQYDQIPVEI(ABA)GHKAIGTVLVGPTPVNIIGRNLL
TQIG(ABA)TLNF
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEELNLPGCWKPKLIGGIAGFIKVRQYDQIPVEIAGHKAIGTVLVGPT
PVNIIGRNLLTQIGATLNFCGGGGPQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEELNLPGCWKPKLIGGIAGFIKV
RQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.03
39.49
VAPOR DIFFUSION, HANGING DROP
6.0
0.1M CITRATE, 0.2M SODIUM PHOPHATE, 30% (W/V) AMMONIUM SULFATE, 10% (V/V) DMSO
, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_sheet
struct_site
chem_comp_atom
chem_comp_bond
entity
pdbx_entity_src_syn
repository
Initial release
Advisory
Atomic model
Database references
Derived calculations
Non-polymer description
Refinement description
Structure summary
Version format compliance
Database references
Other
Refinement description
Data collection
Database references
Derived calculations
Refinement description
Data collection
Source and taxonomy
Structure summary
1
0
2010-01-05
1
1
2011-07-13
1
2
2012-01-11
1
3
2012-12-12
1
4
2017-11-01
1
5
2023-09-06
1
6
2023-11-22
1
7
2024-03-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_sheet.number_strands
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
_entity.details
CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED 203 AMINO ACID 'COVALENT DIMER' HIV-1 PROTEASE MOLECULE
RCSB
Y
RCSB
2009-01-10
REL
REL
2NC
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
HOH
water
Total chemical protein synthesis
sample
THE INHIBITOR HAS A REDUCED PEPTIDE BOND ISOSTERE
[CH2-NH] IN PLACE OF THE SCISSILE AMIDE
2O40
PDB ENTRY 2O40
PDB
experimental model
Inhibitor
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
Peptide-like
ACE
0
2
2NC
2NC
204
A
HOH
2
3
HOH
HOH
205
A
HOH
3
3
HOH
HOH
206
A
HOH
4
3
HOH
HOH
207
A
HOH
5
3
HOH
HOH
208
A
HOH
6
3
HOH
HOH
209
A
HOH
7
3
HOH
HOH
210
A
HOH
8
3
HOH
HOH
211
A
HOH
9
3
HOH
HOH
212
A
HOH
10
3
HOH
HOH
213
A
HOH
11
3
HOH
HOH
214
A
HOH
12
3
HOH
HOH
215
A
HOH
13
3
HOH
HOH
216
A
HOH
14
3
HOH
HOH
217
A
HOH
15
3
HOH
HOH
218
A
HOH
16
3
HOH
HOH
219
A
HOH
17
3
HOH
HOH
220
A
HOH
18
3
HOH
HOH
221
A
HOH
19
3
HOH
HOH
222
A
HOH
20
3
HOH
HOH
223
A
HOH
21
3
HOH
HOH
224
A
HOH
22
3
HOH
HOH
225
A
HOH
23
3
HOH
HOH
226
A
HOH
24
3
HOH
HOH
227
A
HOH
25
3
HOH
HOH
228
A
HOH
26
3
HOH
HOH
229
A
HOH
27
3
HOH
HOH
230
A
HOH
28
3
HOH
HOH
231
A
HOH
29
3
HOH
HOH
232
A
HOH
30
3
HOH
HOH
233
A
HOH
31
3
HOH
HOH
234
A
HOH
32
3
HOH
HOH
235
A
HOH
33
3
HOH
HOH
236
A
HOH
34
3
HOH
HOH
237
A
HOH
35
3
HOH
HOH
238
A
HOH
36
3
HOH
HOH
239
A
HOH
37
3
HOH
HOH
240
A
HOH
38
3
HOH
HOH
241
A
HOH
39
3
HOH
HOH
242
A
HOH
40
3
HOH
HOH
243
A
HOH
41
3
HOH
HOH
244
A
HOH
42
3
HOH
HOH
245
A
HOH
43
3
HOH
HOH
246
A
HOH
44
3
HOH
HOH
247
A
HOH
45
3
HOH
HOH
248
A
HOH
46
3
HOH
HOH
249
A
HOH
47
3
HOH
HOH
250
A
HOH
48
3
HOH
HOH
251
A
HOH
49
3
HOH
HOH
252
A
HOH
50
3
HOH
HOH
253
A
HOH
51
3
HOH
HOH
254
A
HOH
52
3
HOH
HOH
255
A
HOH
53
3
HOH
HOH
256
A
HOH
54
3
HOH
HOH
257
A
HOH
55
3
HOH
HOH
258
A
HOH
56
3
HOH
HOH
259
A
HOH
57
3
HOH
HOH
260
A
HOH
58
3
HOH
HOH
261
A
HOH
59
3
HOH
HOH
262
A
HOH
60
3
HOH
HOH
263
A
HOH
61
3
HOH
HOH
264
A
HOH
62
3
HOH
HOH
265
A
HOH
63
3
HOH
HOH
266
A
HOH
64
3
HOH
HOH
267
A
HOH
65
3
HOH
HOH
268
A
HOH
66
3
HOH
HOH
269
A
HOH
67
3
HOH
HOH
270
A
HOH
68
3
HOH
HOH
271
A
HOH
69
3
HOH
HOH
272
A
HOH
70
3
HOH
HOH
273
A
HOH
71
3
HOH
HOH
274
A
HOH
72
3
HOH
HOH
275
A
HOH
73
3
HOH
HOH
276
A
HOH
74
3
HOH
HOH
277
A
HOH
75
3
HOH
HOH
278
A
HOH
76
3
HOH
HOH
279
A
HOH
77
3
HOH
HOH
280
A
HOH
78
3
HOH
HOH
281
A
HOH
79
3
HOH
HOH
282
A
HOH
80
3
HOH
HOH
283
A
HOH
81
3
HOH
HOH
284
A
HOH
82
3
HOH
HOH
285
A
HOH
83
3
HOH
HOH
286
A
HOH
84
3
HOH
HOH
287
A
HOH
85
3
HOH
HOH
288
A
HOH
86
3
HOH
HOH
289
A
HOH
87
3
HOH
HOH
290
A
HOH
88
3
HOH
HOH
291
A
HOH
89
3
HOH
HOH
292
A
HOH
90
3
HOH
HOH
293
A
HOH
91
3
HOH
HOH
294
A
HOH
92
3
HOH
HOH
295
A
HOH
93
3
HOH
HOH
296
A
HOH
94
3
HOH
HOH
297
A
HOH
95
3
HOH
HOH
298
A
HOH
96
3
HOH
HOH
299
A
HOH
97
3
HOH
HOH
300
A
HOH
98
3
HOH
HOH
301
A
HOH
99
3
HOH
HOH
302
A
HOH
100
3
HOH
HOH
303
A
HOH
101
3
HOH
HOH
304
A
HOH
102
3
HOH
HOH
305
A
HOH
103
3
HOH
HOH
306
A
HOH
104
3
HOH
HOH
307
A
HOH
105
3
HOH
HOH
308
A
HOH
106
3
HOH
HOH
309
A
HOH
107
3
HOH
HOH
310
A
HOH
108
3
HOH
HOH
311
A
HOH
109
3
HOH
HOH
312
A
HOH
110
3
HOH
HOH
313
A
HOH
111
3
HOH
HOH
314
A
HOH
112
3
HOH
HOH
315
A
HOH
113
3
HOH
HOH
316
A
HOH
114
3
HOH
HOH
317
A
HOH
115
3
HOH
HOH
318
A
HOH
116
3
HOH
HOH
319
A
HOH
117
3
HOH
HOH
320
A
HOH
118
3
HOH
HOH
321
A
HOH
1
3
HOH
HOH
322
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
ARG
14
n
14
ARG
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
ILE
33
n
33
ILE
33
A
GLU
34
n
34
GLU
34
A
GLU
35
n
35
GLU
35
A
NLE
36
n
36
NLE
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
YCM
41
n
41
YCM
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
NLE
46
n
46
NLE
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
ALA
51
n
51
ALA
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
PRO
63
n
63
PRO
63
A
VAL
64
n
64
VAL
64
A
GLU
65
n
65
GLU
65
A
ILE
66
n
66
ILE
66
A
ABA
67
n
67
ABA
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
ABA
95
n
95
ABA
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
YCM
100
n
100
YCM
100
A
GLY
101
n
101
GLY
101
A
GLY
102
n
102
GLY
102
A
GLY
103
n
103
GLY
103
A
GLY
104
n
104
GLY
104
A
PRO
105
n
105
PRO
105
A
GLN
106
n
106
GLN
106
A
ILE
107
n
107
ILE
107
A
THR
108
n
108
THR
108
A
LEU
109
n
109
LEU
109
A
TRP
110
n
110
TRP
110
A
LYS
111
n
111
LYS
111
A
ARG
112
n
112
ARG
112
A
PRO
113
n
113
PRO
113
A
LEU
114
n
114
LEU
114
A
VAL
115
n
115
VAL
115
A
THR
116
n
116
THR
116
A
ILE
117
n
117
ILE
117
A
ARG
118
n
118
ARG
118
A
ILE
119
n
119
ILE
119
A
GLY
120
n
120
GLY
120
A
GLY
121
n
121
GLY
121
A
GLN
122
n
122
GLN
122
A
LEU
123
n
123
LEU
123
A
LYS
124
n
124
LYS
124
A
GLU
125
n
125
GLU
125
A
ALA
126
n
126
ALA
126
A
LEU
127
n
127
LEU
127
A
LEU
128
n
128
LEU
128
A
ASP
129
n
129
ASP
129
A
THR
130
n
130
THR
130
A
GLY
131
n
131
GLY
131
A
ALA
132
n
132
ALA
132
A
ASP
133
n
133
ASP
133
A
ASP
134
n
134
ASP
134
A
THR
135
n
135
THR
135
A
VAL
136
n
136
VAL
136
A
ILE
137
n
137
ILE
137
A
GLU
138
n
138
GLU
138
A
GLU
139
n
139
GLU
139
A
NLE
140
n
140
NLE
140
A
ASN
141
n
141
ASN
141
A
LEU
142
n
142
LEU
142
A
PRO
143
n
143
PRO
143
A
GLY
144
n
144
GLY
144
A
YCM
145
n
145
YCM
145
A
TRP
146
n
146
TRP
146
A
LYS
147
n
147
LYS
147
A
PRO
148
n
148
PRO
148
A
LYS
149
n
149
LYS
149
A
NLE
150
n
150
NLE
150
A
ILE
151
n
151
ILE
151
A
GLY
152
n
152
GLY
152
A
GLY
153
n
153
GLY
153
A
ILE
154
n
154
ILE
154
A
ALA
155
n
155
DAL
155
A
GLY
156
n
156
GLY
156
A
PHE
157
n
157
PHE
157
A
ILE
158
n
158
ILE
158
A
LYS
159
n
159
LYS
159
A
VAL
160
n
160
VAL
160
A
ARG
161
n
161
ARG
161
A
GLN
162
n
162
GLN
162
A
TYR
163
n
163
TYR
163
A
ASP
164
n
164
ASP
164
A
GLN
165
n
165
GLN
165
A
ILE
166
n
166
ILE
166
A
PRO
167
n
167
PRO
167
A
VAL
168
n
168
VAL
168
A
GLU
169
n
169
GLU
169
A
ILE
170
n
170
ILE
170
A
ABA
171
n
171
ABA
171
A
GLY
172
n
172
GLY
172
A
HIS
173
n
173
HIS
173
A
LYS
174
n
174
LYS
174
A
ALA
175
n
175
ALA
175
A
ILE
176
n
176
ILE
176
A
GLY
177
n
177
GLY
177
A
THR
178
n
178
THR
178
A
VAL
179
n
179
VAL
179
A
LEU
180
n
180
LEU
180
A
VAL
181
n
181
VAL
181
A
GLY
182
n
182
GLY
182
A
PRO
183
n
183
PRO
183
A
THR
184
n
184
THR
184
A
PRO
185
n
185
PRO
185
A
VAL
186
n
186
VAL
186
A
ASN
187
n
187
ASN
187
A
ILE
188
n
188
ILE
188
A
ILE
189
n
189
ILE
189
A
GLY
190
n
190
GLY
190
A
ARG
191
n
191
ARG
191
A
ASN
192
n
192
ASN
192
A
LEU
193
n
193
LEU
193
A
LEU
194
n
194
LEU
194
A
THR
195
n
195
THR
195
A
GLN
196
n
196
GLN
196
A
ILE
197
n
197
ILE
197
A
GLY
198
n
198
GLY
198
A
ABA
199
n
199
ABA
199
A
THR
200
n
200
THR
200
A
LEU
201
n
201
LEU
201
A
ASN
202
n
202
ASN
202
A
PHE
203
n
203
PHE
203
A
2.3501
-0.8509
0.4832
2.0535
0.6234
1.3060
0.0241
0.0982
-0.0555
0.0313
0.0558
-0.0424
0.0350
0.1324
-0.0799
-0.1160
-0.0017
-0.0033
-0.1238
0.0088
-0.1663
refined
5.0890
1.1810
18.2140
X-RAY DIFFRACTION
A
1
A
203
X-RAY DIFFRACTION
1
software_defined_assembly
PISA
1
monomeric
A
NLE
36
NORLEUCINE
A
NLE
36
LEU
A
YCM
41
S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
A
YCM
41
CYS
A
NLE
46
NORLEUCINE
A
NLE
46
LEU
A
ABA
67
ALPHA-AMINOBUTYRIC ACID
A
ABA
67
ALA
A
ABA
95
ALPHA-AMINOBUTYRIC ACID
A
ABA
95
ALA
A
YCM
100
S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
A
YCM
100
CYS
A
NLE
140
NORLEUCINE
A
NLE
140
LEU
A
YCM
145
S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
A
YCM
145
CYS
A
NLE
150
NORLEUCINE
A
NLE
150
LEU
A
ABA
171
ALPHA-AMINOBUTYRIC ACID
A
ABA
171
ALA
A
ABA
199
ALPHA-AMINOBUTYRIC ACID
A
ABA
199
ALA
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
ILE
3
A
N
ILE
3
A
O
LEU
201
A
O
LEU
201
A
O
THR
200
A
O
THR
200
A
N
ASN
98
A
N
ASN
98
A
N
LEU
97
A
N
LEU
97
A
O
ILE
107
A
O
ILE
107
A
N
LYS
43
A
N
LYS
43
A
O
GLN
58
A
O
GLN
58
A
N
ILE
66
A
N
ILE
66
A
O
HIS
69
A
O
HIS
69
A
O
LEU
76
A
O
LEU
76
A
N
ILE
33
A
N
ILE
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
ARG
14
A
N
ARG
14
A
O
GLU
65
A
O
GLU
65
A
N
LYS
147
A
N
LYS
147
A
O
GLN
162
A
O
GLN
162
A
N
ILE
170
A
N
ILE
170
A
O
HIS
173
A
O
HIS
173
A
O
LEU
180
A
O
LEU
180
A
N
ILE
137
A
N
ILE
137
A
N
VAL
136
A
N
VAL
136
A
O
ILE
188
A
O
ILE
188
A
O
ILE
189
A
O
ILE
189
A
N
LEU
127
A
N
LEU
127
A
O
ALA
126
A
O
ALA
126
A
N
VAL
115
A
N
VAL
115
A
N
ARG
118
A
N
ARG
118
A
O
GLU
169
A
O
GLU
169
1
5.44
0.90
118.30
123.74
A
A
A
CB
CG
OD1
ASP
ASP
ASP
25
25
25
N
1
3.81
0.50
120.30
124.11
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
191
191
191
N
1
A
PRO
39
-54.35
105.22
1
A
ABA
67
36.85
48.17
49.86
25.825
13.87
0.060
0.000
0.000
-0.320
0.000
0.260
0.950
0.939
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.235
0.199
0.201
1.600
20.000
1274
25039
5.100
99.770
1.00
0.50
3.804
0.067
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
0.103
0.103
0.800
0.800
1.400
PDB ENTRY 2O40
MAXIMUM LIKELIHOOD
MASK
1.600
20.000
118
1717
54
0
1545
0.016
0.022
1629
0.001
0.020
1098
1.634
1.990
2203
0.901
3.000
2705
6.412
5.000
204
42.541
24.915
59
12.681
15.000
288
15.876
15.000
9
0.111
0.200
259
0.007
0.020
1750
0.001
0.020
280
0.192
0.200
217
0.195
0.200
1051
0.173
0.200
767
0.088
0.200
874
0.131
0.200
56
0.010
0.200
1
0.115
0.200
5
0.177
0.200
35
0.158
0.200
6
1.081
1.500
1062
0.320
1.500
431
1.617
2.000
1674
2.449
3.000
638
3.694
4.500
529
0.329
0.265
1.639
102
1654
1756
1654
20
97.500
1.600
50.000
3FSM
25109
25109
81.1
0.079
1.530
1
22.636
4.900
99.800
0.677
1.60
1.66
2.9
2419
1.580
1
4.80
98.30
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
package
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
package
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.2.0019
data extraction
PDB
help@deposit.rcsb.org
June 11, 2008
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.006
phasing
MOLREP
CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED 203 AMINO ACID 'COVALENT DIMER' [L-Ala51,D-Ala51'] HIV-1 PROTEASE MOLECULE
1
N
N
2
N
N
3
N
N
A
GLY
86
A
GLY
86
HELX_P
A
THR
91
A
THR
91
1
1
6
A
YCM
100
A
YCM
100
HELX_P
A
GLY
103
A
GLY
103
5
2
4
A
GLY
190
A
GLY
190
HELX_P
A
THR
195
A
THR
195
1
3
6
covale
1.329
both
A
GLU
35
A
C
GLU
35
1_555
A
NLE
36
A
N
NLE
36
1_555
covale
1.327
both
A
NLE
36
A
C
NLE
36
1_555
A
ASN
37
A
N
ASN
37
1_555
covale
1.324
both
A
GLY
40
A
C
GLY
40
1_555
A
YCM
41
A
N
YCM
41
1_555
covale
1.334
both
A
YCM
41
A
C
YCM
41
1_555
A
TRP
42
A
N
TRP
42
1_555
covale
1.339
both
A
LYS
45
A
C
LYS
45
1_555
A
NLE
46
A
N
NLE
46
1_555
covale
1.336
both
A
NLE
46
A
C
NLE
46
1_555
A
ILE
47
A
N
ILE
47
1_555
covale
1.333
both
A
ILE
66
A
C
ILE
66
1_555
A
ABA
67
A
N
ABA
67
1_555
covale
1.327
both
A
ABA
67
A
C
ABA
67
1_555
A
GLY
68
A
N
GLY
68
1_555
covale
1.315
both
A
GLY
94
A
C
GLY
94
1_555
A
ABA
95
A
N
ABA
95
1_555
covale
1.345
both
A
ABA
95
A
C
ABA
95
1_555
A
THR
96
A
N
THR
96
1_555
covale
1.335
both
A
PHE
99
A
C
PHE
99
1_555
A
YCM
100
A
N
YCM
100
1_555
covale
1.334
both
A
YCM
100
A
C
YCM
100
1_555
A
GLY
101
A
N
GLY
101
1_555
covale
1.329
both
A
GLU
139
A
C
GLU
139
1_555
A
NLE
140
A
N
NLE
140
1_555
covale
1.331
both
A
NLE
140
A
C
NLE
140
1_555
A
ASN
141
A
N
ASN
141
1_555
covale
1.356
both
A
GLY
144
A
C
GLY
144
1_555
A
YCM
145
A
N
YCM
145
1_555
covale
1.319
both
A
YCM
145
A
C
YCM
145
1_555
A
TRP
146
A
N
TRP
146
1_555
covale
1.328
both
A
LYS
149
A
C
LYS
149
1_555
A
NLE
150
A
N
NLE
150
1_555
covale
1.327
both
A
NLE
150
A
C
NLE
150
1_555
A
ILE
151
A
N
ILE
151
1_555
covale
1.346
both
A
ILE
154
A
C
ILE
154
1_555
A
DAL
155
A
N
DAL
155
1_555
covale
1.330
both
A
DAL
155
A
C
DAL
155
1_555
A
GLY
156
A
N
GLY
156
1_555
covale
1.337
both
A
ILE
170
A
C
ILE
170
1_555
A
ABA
171
A
N
ABA
171
1_555
covale
1.331
both
A
ABA
171
A
C
ABA
171
1_555
A
GLY
172
A
N
GLY
172
1_555
covale
1.337
both
A
GLY
198
A
C
GLY
198
1_555
A
ABA
199
A
N
ABA
199
1_555
covale
1.326
both
A
ABA
199
A
C
ABA
199
1_555
A
THR
200
A
N
THR
200
1_555
HYDROLASE/HYDROLASE INHIBITOR
asymmetric dimer, covalent dimer, beta-sheet, HYDROLASE-HYDROLASE INHIBITOR complex
3FSM
PDB
1
1
3FSM
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEELNLPGCWKPKLIGGIAGFIKVRQYDQIPVEIAGHKAIGTVLVGPT
PVNIIGRNLLTQIGATLNFCGGGGPQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEELNLPGCWKPKLIGGIXGFIKV
RQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
1
203
3FSM
1
203
3FSM
A
1
1
203
4
8
8
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
GLN
2
A
GLN
2
A
ILE
3
A
ILE
3
A
THR
200
A
THR
200
A
ASN
202
A
ASN
202
A
THR
96
A
THR
96
A
ASN
98
A
ASN
98
A
GLN
106
A
GLN
106
A
ILE
107
A
ILE
107
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
ILE
33
A
ILE
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
A
LYS
147
A
LYS
147
A
GLY
153
A
GLY
153
A
GLY
156
A
GLY
156
A
ILE
170
A
ILE
170
A
HIS
173
A
HIS
173
A
VAL
181
A
VAL
181
A
VAL
136
A
VAL
136
A
ILE
137
A
ILE
137
A
ILE
188
A
ILE
188
A
ILE
189
A
ILE
189
A
GLN
122
A
GLN
122
A
LEU
128
A
LEU
128
A
LEU
114
A
LEU
114
A
ILE
119
A
ILE
119
A
GLY
156
A
GLY
156
A
ILE
170
A
ILE
170
BINDING SITE FOR RESIDUE DAL A 155
A
DAL
155
Software
7
BINDING SITE FOR RESIDUE 2NC A 204
A
2NC
204
Software
24
A
ALA
51
A
ALA
51
7
1_555
A
GLY
52
A
GLY
52
7
1_555
A
PHE
53
A
PHE
53
7
1_555
A
GLY
153
A
GLY
153
7
1_555
A
ILE
154
A
ILE
154
7
1_555
A
GLY
156
A
GLY
156
7
1_555
A
HOH
274
C
HOH
7
1_555
A
ASP
25
A
ASP
25
24
1_555
A
GLY
27
A
GLY
27
24
1_555
A
ALA
28
A
ALA
28
24
1_555
A
ASP
29
A
ASP
29
24
1_555
A
ASP
30
A
ASP
30
24
1_555
A
ILE
47
A
ILE
47
24
1_555
A
GLY
48
A
GLY
48
24
1_555
A
GLY
49
A
GLY
49
24
1_555
A
ILE
50
A
ILE
50
24
1_555
A
VAL
82
A
VAL
82
24
1_555
A
ASP
129
A
ASP
129
24
1_555
A
GLY
131
A
GLY
131
24
1_555
A
ALA
132
A
ALA
132
24
1_555
A
ASP
133
A
ASP
133
24
1_555
A
ASP
134
A
ASP
134
24
1_555
A
GLY
152
A
GLY
152
24
1_555
A
ILE
154
A
ILE
154
24
1_555
A
PRO
185
A
PRO
185
24
1_555
A
VAL
186
A
VAL
186
24
1_555
A
ILE
188
A
ILE
188
24
1_555
A
HOH
205
C
HOH
24
1_555
A
HOH
208
C
HOH
24
1_555
A
HOH
248
C
HOH
24
1_555
A
HOH
312
C
HOH
24
1_555
19
P 21 21 21