0.019331
0.000000
0.000000
0.000000
0.016925
0.000000
0.000000
0.000000
0.016324
0.00000
0.00000
0.00000
Schiffer, C.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
51.731
59.083
61.259
C2 H3 O2 -1
59.044
ACETATE ION
non-polymer
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
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
N
5
N
H
N
6
N
H
N
7
N
H
N
8
N
N
N
9
S
C
N
10
N
C
N
11
N
O
N
12
N
C
N
13
N
O
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
N
N
22
S
C
N
23
N
C
N
24
N
O
N
25
N
C
N
26
N
C
N
27
N
C
N
28
N
N
N
29
N
C
N
30
N
N
N
31
N
N
N
32
N
O
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
N
N
49
S
C
N
50
N
C
N
51
N
O
N
52
N
C
N
53
N
C
N
54
N
O
N
55
N
N
N
56
N
O
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
N
N
66
S
C
N
67
N
C
N
68
N
O
N
69
N
C
N
70
N
C
N
71
N
O
N
72
N
O
N
73
N
O
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
N
N
82
R
C
N
83
N
C
N
84
N
O
N
85
N
C
N
86
N
S
N
87
N
O
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
N
N
96
S
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
C
N
101
N
C
N
102
N
O
N
103
N
N
N
104
N
O
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
N
N
116
S
C
N
117
N
C
N
118
N
O
N
119
N
C
N
120
N
C
N
121
N
C
N
122
N
O
N
123
N
O
N
124
N
O
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
H
N
132
N
H
N
133
N
H
N
134
N
N
N
135
N
C
N
136
N
C
N
137
N
O
N
138
N
O
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
Y
149
N
C
Y
150
N
N
Y
151
N
C
Y
152
N
C
Y
153
N
N
N
154
N
O
N
155
N
H
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
O
N
166
N
H
N
167
N
H
N
168
N
N
N
169
S
C
N
170
N
C
N
171
N
O
N
172
S
C
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
O
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
N
N
191
S
C
N
192
N
C
N
193
N
O
N
194
N
C
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
O
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
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
S
C
N
214
N
C
N
215
N
O
N
216
N
C
N
217
N
C
N
218
N
C
N
219
N
C
N
220
N
N
N
221
N
O
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
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
N
N
238
S
C
N
239
N
C
N
240
N
O
N
241
N
C
N
242
N
C
N
243
N
S
N
244
N
C
N
245
N
O
N
246
N
H
N
247
N
H
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
S
C
N
259
N
C
N
260
N
O
N
261
N
C
Y
262
N
C
Y
263
N
C
Y
264
N
C
Y
265
N
C
Y
266
N
C
Y
267
N
C
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
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
N
285
N
C
N
286
N
C
N
287
N
O
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
H
N
296
N
H
N
297
N
N
N
298
S
C
N
299
N
C
N
300
N
O
N
301
R
C
N
302
N
O
N
303
N
C
N
304
N
O
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
N
N
315
S
C
N
316
N
C
N
317
N
O
N
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
Y
322
N
N
Y
323
N
C
Y
324
N
C
Y
325
N
C
Y
326
N
C
Y
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
N
N
342
S
C
N
343
N
C
N
344
N
O
N
345
N
C
Y
346
N
C
Y
347
N
C
Y
348
N
C
Y
349
N
C
Y
350
N
C
Y
351
N
C
N
352
N
O
N
353
N
O
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
N
N
366
S
C
N
367
N
C
N
368
N
O
N
369
N
C
N
370
N
C
N
371
N
C
N
372
N
O
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
H
N
381
N
H
N
382
N
H
N
383
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
sing
N
12
N
sing
N
13
N
doub
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
sing
N
25
N
doub
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
doub
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
doub
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
doub
N
57
N
sing
N
58
N
sing
N
59
N
sing
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
doub
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
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
N
80
N
sing
N
81
N
sing
N
82
N
doub
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
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
doub
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
sing
N
114
N
doub
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
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
doub
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
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
Y
146
N
sing
Y
147
N
doub
Y
148
N
doub
N
149
N
sing
Y
150
N
sing
N
151
N
sing
Y
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
doub
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
doub
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
doub
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
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
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
sing
N
249
N
doub
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
Y
254
N
doub
Y
255
N
sing
Y
256
N
sing
N
257
N
sing
Y
258
N
doub
N
259
N
sing
Y
260
N
doub
N
261
N
sing
Y
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
sing
N
271
N
sing
N
272
N
doub
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
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
sing
N
287
N
sing
N
288
N
sing
N
289
N
doub
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
doub
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
Y
310
N
doub
Y
311
N
sing
Y
312
N
sing
N
313
N
sing
Y
314
N
doub
Y
315
N
sing
Y
316
N
sing
N
317
N
sing
Y
318
N
sing
Y
319
N
doub
N
320
N
sing
Y
321
N
doub
N
322
N
sing
Y
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
Y
338
N
doub
Y
339
N
sing
Y
340
N
sing
N
341
N
sing
Y
342
N
doub
N
343
N
sing
Y
344
N
doub
N
345
N
sing
Y
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
UK
Structure
STRUE6
2005
0969-2126
10
369
381
10.1016/S0969-2126(02)00720-7
12005435
Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes.
2002
10.2210/pdb1kjh/pdb
pdb_00001kjh
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298.0
1
MIRRORS
IMAGE PLATE
2000-01-25
RIGAKU
YALE MIRRORS
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
1.5418
ROTATING ANODE
RIGAKU
10800.777
POL POLYPROTEIN
3.4.23.16
HIV-1 PROTEASE, RESIDUES 57-155
D25N,Q7K
2
man
polymer
1189.491
POL POLYPROTEIN
RNASE H-INTEGRASE SUBSTRATE PEPTIDE, RESIDUES 723-732
1
syn
polymer
59.044
ACETATE ION
2
syn
non-polymer
18.015
water
84
nat
water
no
no
PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
A,B
polypeptide(L)
no
no
IRKILFLDGI
IRKILFLDGI
P
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
Lentivirus
Escherichia
sample
POL
11676
Human immunodeficiency virus 1
562
Escherichia coli
1
2.05
40.07
VAPOR DIFFUSION, HANGING DROP
AMMONIUM SULPHATE, SODIUM CITRATE, SODIUM PHOSPHATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
database_2
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Data collection
Refinement description
1
0
2002-03-06
1
1
2008-04-27
1
2
2011-07-13
1
3
2021-10-27
1
4
2023-08-16
_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
HOW DOES A SYMMETRIC DIMER RECOGNIZE AN ASYMMETRIC SUBSTRATE? A SUBSTRATE COMPLEX OF HIV-1 PROTEASE
SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES
SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES
SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES
SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES
RCSB
Y
RCSB
2001-12-04
REL
ACT
ACETATE ION
HOH
water
1F7A
PDB ENTRY 1F7A
PDB
experimental model
ACE
502
3
ACT
ACT
502
B
ACE
501
3
ACT
ACT
501
P
WAT
4
4
HOH
HOH
100
A
WAT
9
4
HOH
HOH
101
A
WAT
12
4
HOH
HOH
102
A
WAT
13
4
HOH
HOH
103
A
WAT
16
4
HOH
HOH
104
A
WAT
18
4
HOH
HOH
105
A
WAT
19
4
HOH
HOH
106
A
WAT
21
4
HOH
HOH
107
A
WAT
22
4
HOH
HOH
108
A
WAT
23
4
HOH
HOH
109
A
WAT
31
4
HOH
HOH
110
A
WAT
32
4
HOH
HOH
111
A
WAT
33
4
HOH
HOH
112
A
WAT
34
4
HOH
HOH
113
A
WAT
39
4
HOH
HOH
114
A
WAT
40
4
HOH
HOH
115
A
WAT
41
4
HOH
HOH
116
A
WAT
44
4
HOH
HOH
117
A
WAT
47
4
HOH
HOH
118
A
WAT
48
4
HOH
HOH
119
A
WAT
49
4
HOH
HOH
120
A
WAT
50
4
HOH
HOH
121
A
WAT
51
4
HOH
HOH
122
A
WAT
52
4
HOH
HOH
123
A
WAT
53
4
HOH
HOH
124
A
WAT
54
4
HOH
HOH
125
A
WAT
55
4
HOH
HOH
126
A
WAT
59
4
HOH
HOH
127
A
WAT
64
4
HOH
HOH
128
A
WAT
65
4
HOH
HOH
129
A
WAT
66
4
HOH
HOH
130
A
WAT
67
4
HOH
HOH
131
A
WAT
68
4
HOH
HOH
132
A
WAT
69
4
HOH
HOH
133
A
WAT
70
4
HOH
HOH
134
A
WAT
71
4
HOH
HOH
135
A
WAT
72
4
HOH
HOH
136
A
WAT
74
4
HOH
HOH
137
A
WAT
75
4
HOH
HOH
138
A
WAT
76
4
HOH
HOH
139
A
WAT
77
4
HOH
HOH
140
A
WAT
79
4
HOH
HOH
141
A
WAT
82
4
HOH
HOH
142
A
WAT
83
4
HOH
HOH
143
A
WAT
84
4
HOH
HOH
144
A
WAT
1
4
HOH
HOH
503
B
WAT
2
4
HOH
HOH
504
B
WAT
5
4
HOH
HOH
505
B
WAT
6
4
HOH
HOH
506
B
WAT
7
4
HOH
HOH
507
B
WAT
8
4
HOH
HOH
508
B
WAT
10
4
HOH
HOH
509
B
WAT
11
4
HOH
HOH
510
B
WAT
14
4
HOH
HOH
511
B
WAT
15
4
HOH
HOH
512
B
WAT
17
4
HOH
HOH
513
B
WAT
20
4
HOH
HOH
514
B
WAT
24
4
HOH
HOH
515
B
WAT
25
4
HOH
HOH
516
B
WAT
27
4
HOH
HOH
517
B
WAT
28
4
HOH
HOH
518
B
WAT
29
4
HOH
HOH
519
B
WAT
30
4
HOH
HOH
520
B
WAT
36
4
HOH
HOH
521
B
WAT
37
4
HOH
HOH
522
B
WAT
42
4
HOH
HOH
523
B
WAT
43
4
HOH
HOH
524
B
WAT
45
4
HOH
HOH
525
B
WAT
46
4
HOH
HOH
526
B
WAT
56
4
HOH
HOH
527
B
WAT
57
4
HOH
HOH
528
B
WAT
58
4
HOH
HOH
529
B
WAT
60
4
HOH
HOH
530
B
WAT
61
4
HOH
HOH
531
B
WAT
62
4
HOH
HOH
532
B
WAT
63
4
HOH
HOH
533
B
WAT
78
4
HOH
HOH
534
B
WAT
80
4
HOH
HOH
535
B
WAT
81
4
HOH
HOH
536
B
WAT
85
4
HOH
HOH
537
B
WAT
86
4
HOH
HOH
538
B
WAT
3
4
HOH
HOH
502
P
WAT
35
4
HOH
HOH
503
P
WAT
87
4
HOH
HOH
504
P
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
ASN
25
n
25
ASN
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
ALA
41
n
41
LYS
41
A
TRP
42
n
42
TRP
42
A
ALA
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
ALA
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
CYS
67
n
67
CYS
67
A
GLY
68
n
68
GLY
68
A
HIS
69
n
69
HIS
69
A
ALA
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
PRO
1
n
1
PRO
1
B
GLN
2
n
2
GLN
2
B
ILE
3
n
3
ILE
3
B
THR
4
n
4
THR
4
B
LEU
5
n
5
LEU
5
B
TRP
6
n
6
TRP
6
B
ALA
7
n
7
LYS
7
B
ARG
8
n
8
ARG
8
B
PRO
9
n
9
PRO
9
B
LEU
10
n
10
LEU
10
B
VAL
11
n
11
VAL
11
B
THR
12
n
12
THR
12
B
ILE
13
n
13
ILE
13
B
ARG
14
n
14
ARG
14
B
ILE
15
n
15
ILE
15
B
GLY
16
n
16
GLY
16
B
GLY
17
n
17
GLY
17
B
GLN
18
n
18
GLN
18
B
LEU
19
n
19
LEU
19
B
LYS
20
n
20
LYS
20
B
GLU
21
n
21
GLU
21
B
ALA
22
n
22
ALA
22
B
LEU
23
n
23
LEU
23
B
LEU
24
n
24
LEU
24
B
ASN
25
n
25
ASN
25
B
THR
26
n
26
THR
26
B
GLY
27
n
27
GLY
27
B
ALA
28
n
28
ALA
28
B
ASP
29
n
29
ASP
29
B
ASP
30
n
30
ASP
30
B
THR
31
n
31
THR
31
B
VAL
32
n
32
VAL
32
B
LEU
33
n
33
LEU
33
B
GLU
34
n
34
GLU
34
B
GLU
35
n
35
GLU
35
B
MET
36
n
36
MET
36
B
ASN
37
n
37
ASN
37
B
LEU
38
n
38
LEU
38
B
PRO
39
n
39
PRO
39
B
GLY
40
n
40
GLY
40
B
ALA
41
n
41
LYS
41
B
TRP
42
n
42
TRP
42
B
ALA
43
n
43
LYS
43
B
PRO
44
n
44
PRO
44
B
ALA
45
n
45
LYS
45
B
MET
46
n
46
MET
46
B
ILE
47
n
47
ILE
47
B
GLY
48
n
48
GLY
48
B
GLY
49
n
49
GLY
49
B
ILE
50
n
50
ILE
50
B
GLY
51
n
51
GLY
51
B
GLY
52
n
52
GLY
52
B
PHE
53
n
53
PHE
53
B
ILE
54
n
54
ILE
54
B
ALA
55
n
55
LYS
55
B
VAL
56
n
56
VAL
56
B
ARG
57
n
57
ARG
57
B
GLN
58
n
58
GLN
58
B
TYR
59
n
59
TYR
59
B
ASP
60
n
60
ASP
60
B
GLN
61
n
61
GLN
61
B
ILE
62
n
62
ILE
62
B
PRO
63
n
63
PRO
63
B
VAL
64
n
64
VAL
64
B
GLU
65
n
65
GLU
65
B
ILE
66
n
66
ILE
66
B
CYS
67
n
67
CYS
67
B
GLY
68
n
68
GLY
68
B
HIS
69
n
69
HIS
69
B
ALA
70
n
70
LYS
70
B
ALA
71
n
71
ALA
71
B
ILE
72
n
72
ILE
72
B
GLY
73
n
73
GLY
73
B
THR
74
n
74
THR
74
B
VAL
75
n
75
VAL
75
B
LEU
76
n
76
LEU
76
B
VAL
77
n
77
VAL
77
B
GLY
78
n
78
GLY
78
B
PRO
79
n
79
PRO
79
B
THR
80
n
80
THR
80
B
PRO
81
n
81
PRO
81
B
VAL
82
n
82
VAL
82
B
ASN
83
n
83
ASN
83
B
ILE
84
n
84
ILE
84
B
ILE
85
n
85
ILE
85
B
GLY
86
n
86
GLY
86
B
ARG
87
n
87
ARG
87
B
ASN
88
n
88
ASN
88
B
LEU
89
n
89
LEU
89
B
LEU
90
n
90
LEU
90
B
THR
91
n
91
THR
91
B
GLN
92
n
92
GLN
92
B
ILE
93
n
93
ILE
93
B
GLY
94
n
94
GLY
94
B
CYS
95
n
95
CYS
95
B
THR
96
n
96
THR
96
B
LEU
97
n
97
LEU
97
B
ASN
98
n
98
ASN
98
B
PHE
99
n
99
PHE
99
B
ILE
1
n
1
ILE
1
P
ARG
2
n
2
ARG
2
P
LYS
3
n
3
LYS
3
P
ILE
4
n
4
ILE
4
P
LEU
5
n
5
LEU
5
P
PHE
6
n
6
PHE
6
P
LEU
7
n
7
LEU
7
P
ASP
8
n
8
ASP
8
P
GLY
9
n
9
GLY
9
P
ALA
10
n
10
ILE
10
P
author_and_software_defined_assembly
PISA
3
trimeric
5980
-33
9060
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
B
O
LEU
97
B
O
LEU
97
B
O
ASN
98
B
O
ASN
98
A
N
THR
96
A
N
THR
96
A
O
LEU
97
A
O
LEU
97
B
N
ILE
3
B
N
ILE
3
A
O
ILE
47
A
O
ILE
47
A
N
ILE
54
A
N
ILE
54
A
N
GLU
65
A
N
GLU
65
A
O
ARG
14
A
O
ARG
14
A
O
ILE
15
A
O
ILE
15
A
N
GLN
18
A
N
GLN
18
A
O
LEU
23
A
O
LEU
23
A
N
ILE
85
A
N
ILE
85
A
N
ILE
84
A
N
ILE
84
A
O
VAL
32
A
O
VAL
32
A
N
LEU
33
A
N
LEU
33
A
O
LEU
76
A
O
LEU
76
A
O
VAL
77
A
O
VAL
77
A
N
ARG
57
A
N
ARG
57
B
O
GLY
49
B
O
GLY
49
B
N
GLY
52
B
N
GLY
52
B
N
GLU
65
B
N
GLU
65
B
O
ARG
14
B
O
ARG
14
B
N
ILE
15
B
N
ILE
15
B
O
GLN
18
B
O
GLN
18
B
O
LEU
23
B
O
LEU
23
B
N
ILE
85
B
N
ILE
85
B
N
ILE
84
B
N
ILE
84
B
O
VAL
32
B
O
VAL
32
B
N
LEU
33
B
N
LEU
33
B
O
LEU
76
B
O
LEU
76
B
O
VAL
77
B
O
VAL
77
B
N
ARG
57
B
N
ARG
57
1
A
CG
LYS
41
A
CG
LYS
41
1
Y
1
A
CD
LYS
41
A
CD
LYS
41
1
Y
1
A
CE
LYS
41
A
CE
LYS
41
1
Y
1
A
NZ
LYS
41
A
NZ
LYS
41
1
Y
1
A
CG
LYS
43
A
CG
LYS
43
1
Y
1
A
CD
LYS
43
A
CD
LYS
43
1
Y
1
A
CE
LYS
43
A
CE
LYS
43
1
Y
1
A
NZ
LYS
43
A
NZ
LYS
43
1
Y
1
A
CG
LYS
55
A
CG
LYS
55
1
Y
1
A
CD
LYS
55
A
CD
LYS
55
1
Y
1
A
CE
LYS
55
A
CE
LYS
55
1
Y
1
A
NZ
LYS
55
A
NZ
LYS
55
1
Y
1
A
CG
LYS
70
A
CG
LYS
70
1
Y
1
A
CD
LYS
70
A
CD
LYS
70
1
Y
1
A
CE
LYS
70
A
CE
LYS
70
1
Y
1
A
NZ
LYS
70
A
NZ
LYS
70
1
Y
1
B
CG
LYS
7
B
CG
LYS
7
1
Y
1
B
CD
LYS
7
B
CD
LYS
7
1
Y
1
B
CE
LYS
7
B
CE
LYS
7
1
Y
1
B
NZ
LYS
7
B
NZ
LYS
7
1
Y
1
B
CG
LYS
41
B
CG
LYS
41
1
Y
1
B
CD
LYS
41
B
CD
LYS
41
1
Y
1
B
CE
LYS
41
B
CE
LYS
41
1
Y
1
B
NZ
LYS
41
B
NZ
LYS
41
1
Y
1
B
CG
LYS
43
B
CG
LYS
43
1
Y
1
B
CD
LYS
43
B
CD
LYS
43
1
Y
1
B
CE
LYS
43
B
CE
LYS
43
1
Y
1
B
NZ
LYS
43
B
NZ
LYS
43
1
Y
1
B
CG
LYS
45
B
CG
LYS
45
1
Y
1
B
CD
LYS
45
B
CD
LYS
45
1
Y
1
B
CE
LYS
45
B
CE
LYS
45
1
Y
1
B
NZ
LYS
45
B
NZ
LYS
45
1
Y
1
B
CG
LYS
55
B
CG
LYS
55
1
Y
1
B
CD
LYS
55
B
CD
LYS
55
1
Y
1
B
CE
LYS
55
B
CE
LYS
55
1
Y
1
B
NZ
LYS
55
B
NZ
LYS
55
1
Y
1
B
CG
LYS
70
B
CG
LYS
70
1
Y
1
B
CD
LYS
70
B
CD
LYS
70
1
Y
1
B
CE
LYS
70
B
CE
LYS
70
1
Y
1
B
NZ
LYS
70
B
NZ
LYS
70
1
Y
1
P
CG1
ILE
10
C
CG1
ILE
10
1
Y
1
P
CG2
ILE
10
C
CG2
ILE
10
1
Y
1
P
CD1
ILE
10
C
CD1
ILE
10
1
Y
1
A
GLU
35
8.55
113.91
1
A
GLU
35
7.49
113.91
1
A
MET
36
-176.27
124.18
1
P
LEU
5
-92.53
49.44
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
ACE.PARAM
ACE.TOP
24.4
-2.59
0.00
0.00
0.82
0.00
1.77
0.2270000
0.006
0.1880000
0.1880000
2.00
32.85
1287
12905
12905
10.3
97.5
RANDOM
164979.87
0.000000
1
RESTRAINED
THROUGHOUT
0.0
FOURIER SYNTHESIS
PDB ENTRY 1F7A
ENGH & HUBER
FLAT MODEL
63.3476
0.349263
0.26
0.21
5.00
0.20
0.16
2.00
32.85
84
1675
8
0
1583
0.006
2.7
26.6
0.87
19.4
2.000
32.85
1KJH
12905
12905
0
0
0.0690000
1
8.5000
7.50
97.5
refinement
CNS
data reduction
DENZO
data scaling
SCALEPACK
phasing
CNS
SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
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
B
GLY
86
B
GLY
86
HELX_P
B
THR
91
B
THR
91
1
3
6
HYDROLASE
RNASE H, INTEGRASE, SUBSTRATE RECOGNITION, HYDROLASE
POL_HV1A2
UNP
1
1
P03369
FFREDLAFLQGKAREFSSEQTRANSPTRRELQVWGGENNSLSEAGADRQGTVSFNFPQITLWQRPLVTIRIGGQLKEALL
DTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPISPI
ETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQ
DFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMT
KILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIM
LPEKDSWTVNDIQKLVGKLNWASQIYAGIKVKQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHEVYYDPSKDL
VAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKVSTESIVIWGKIPKFKLPIQKETWEAWWMEY
WQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTDRGRQKVVSIADTTNQKTELQAIHLA
LQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLNGI
DKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKIILVAVHVASGYIE
AEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVVESMNNELKKIIGQV
RDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDNKDPLWKGPAKLLWKG
EGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED
POL_HV1PV
UNP
2
723
P03368
IRKILFLDGI
57
155
1KJH
1
99
P03369
A
1
1
99
57
155
1KJH
1
99
P03369
B
1
1
99
723
732
1KJH
1
10
P03368
P
2
1
10
1
GLN
engineered mutation
LYS
7
1KJH
A
P03369
UNP
63
7
1
ASP
engineered mutation
ASN
25
1KJH
A
P03369
UNP
81
25
2
GLN
engineered mutation
LYS
7
1KJH
B
P03369
UNP
63
7
2
ASP
engineered mutation
ASN
25
1KJH
B
P03369
UNP
81
25
4
8
8
anti-parallel
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
A
GLN
2
A
GLN
2
A
ILE
3
A
ILE
3
B
THR
96
B
THR
96
B
ASN
98
B
ASN
98
A
THR
96
A
THR
96
A
ASN
98
A
ASN
98
B
GLN
2
B
GLN
2
B
ILE
3
B
ILE
3
A
LYS
43
A
LYS
43
A
GLY
48
A
GLY
48
A
PHE
53
A
PHE
53
A
ILE
66
A
ILE
66
A
LEU
10
A
LEU
10
A
ILE
15
A
ILE
15
A
GLN
18
A
GLN
18
A
LEU
24
A
LEU
24
A
ILE
84
A
ILE
84
A
ILE
85
A
ILE
85
A
VAL
32
A
VAL
32
A
LEU
33
A
LEU
33
A
HIS
69
A
HIS
69
A
VAL
77
A
VAL
77
A
PHE
53
A
PHE
53
A
ILE
66
A
ILE
66
B
LYS
43
B
LYS
43
B
GLY
49
B
GLY
49
B
GLY
52
B
GLY
52
B
ILE
66
B
ILE
66
B
LEU
10
B
LEU
10
B
ILE
15
B
ILE
15
B
GLN
18
B
GLN
18
B
LEU
24
B
LEU
24
B
ILE
84
B
ILE
84
B
ILE
85
B
ILE
85
B
VAL
32
B
VAL
32
B
LEU
33
B
LEU
33
B
HIS
69
B
HIS
69
B
VAL
77
B
VAL
77
B
GLY
52
B
GLY
52
B
ILE
66
B
ILE
66
BINDING SITE FOR RESIDUE ACT P 501
P
ACT
501
Software
3
BINDING SITE FOR RESIDUE ACT B 502
B
ACT
502
Software
3
A
ARG
8
A
ARG
8
3
1_555
P
ILE
1
C
ILE
1
3
1_555
P
ARG
2
C
ARG
2
3
1_555
A
PRO
1
A
PRO
1
3
4_456
B
HIS
69
B
HIS
69
3
1_555
B
LYS
70
B
LYS
70
3
1_555
19
P 21 21 21