0.020414
0.000000
0.000000
0.000000
0.020414
0.000000
0.000000
0.000000
0.009468
0.00000
0.00000
0.00000
Heaslet, H.
Tam, K.
Elder, J.H.
Stout, C.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
48.985
48.985
105.620
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
C3 H8 O2
76.094
R-1,2-PROPANEDIOL
non-polymer
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
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
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
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
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
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
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
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
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
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
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
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
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
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
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
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
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
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
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
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
MG
N
251
N
C
N
252
R
C
N
253
N
C
N
254
N
O
N
255
N
O
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
S
C
N
266
N
C
N
267
N
O
N
268
N
C
Y
269
N
C
Y
270
N
C
Y
271
N
C
Y
272
N
C
Y
273
N
C
Y
274
N
C
N
275
N
O
N
276
N
H
N
277
N
H
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
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
N
C
N
292
N
C
N
293
N
C
N
294
N
O
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
R
C
N
309
N
O
N
310
N
C
N
311
N
O
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
H
N
321
N
N
N
322
S
C
N
323
N
C
N
324
N
O
N
325
N
C
Y
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
N
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
N
335
N
O
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
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
N
359
N
O
N
360
N
O
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
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
N
N
373
S
C
N
374
N
C
N
375
N
O
N
376
N
C
N
377
N
C
N
378
N
C
N
379
N
O
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
H
N
390
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
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
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
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
doub
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
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
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
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
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
doub
N
77
N
sing
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
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
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
doub
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
doub
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
doub
N
127
N
sing
N
128
N
sing
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
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
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
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
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
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
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
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
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
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
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
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
doub
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
Y
260
N
doub
Y
261
N
sing
Y
262
N
sing
N
263
N
sing
Y
264
N
doub
N
265
N
sing
Y
266
N
doub
N
267
N
sing
Y
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
doub
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
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
doub
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
doub
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
Y
316
N
doub
Y
317
N
sing
Y
318
N
sing
N
319
N
sing
Y
320
N
doub
Y
321
N
sing
Y
322
N
sing
N
323
N
sing
Y
324
N
sing
Y
325
N
doub
N
326
N
sing
Y
327
N
doub
N
328
N
sing
Y
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
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
doub
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
Y
344
N
doub
Y
345
N
sing
Y
346
N
sing
N
347
N
sing
Y
348
N
doub
N
349
N
sing
Y
350
N
doub
N
351
N
sing
Y
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
doub
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
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
63
866
875
10.1107/S0907444907029125
17642513
Conformational flexibility in the flap domains of ligand-free HIV protease.
2007
10.2210/pdb2hb4/pdb
pdb_00002hb4
100
1
Rigaku VariMax HF Confocal Mirror
CCD
2006-05-02
RIGAKU SATURN 92
Rigaku VariMax HF Confocal Mirror
SINGLE WAVELENGTH
M
x-ray
1
1.54
1.0
1.54
ROTATING ANODE
RIGAKU
10831.833
Protease
3.4.23.16
residues 500-598
Q7K
1
man
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
76.094
R-1,2-PROPANEDIOL
3
syn
non-polymer
18.015
water
41
nat
water
no
no
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Lentivirus
NL4-3
Escherichia
sample
gag-pol
11676
Human immunodeficiency virus 1
562
Escherichia coli
BL21.DE3, PLYS S
PLASMID
PET 21A+
1
2.92
57.92
VAPOR DIFFUSION, HANGING DROP
8.5
100mM Tris HCl, 0.2M MgCl2, 15% PEG 8K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281.16K
281.16
pdbx_unobs_or_zero_occ_atoms
software
database_2
pdbx_struct_conn_angle
pdbx_unobs_or_zero_occ_atoms
struct_conn
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Advisory
Derived calculations
Version format compliance
Advisory
Data collection
Refinement description
Advisory
Database references
Derived calculations
Data collection
1
0
2007-06-26
1
1
2008-05-01
1
2
2011-07-13
1
3
2019-07-24
1
4
2021-10-20
1
5
2024-02-14
_software.classification
_software.contact_author
_software.contact_author_email
_software.date
_software.location
_software.name
_software.type
_software.version
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_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 HIV protease 6X mutant in unliganded state.
Structure of wild-type HIV protease in complex with TL-3.
RCSB
Y
RCSB
2006-06-13
REL
REL
MG
MAGNESIUM ION
PGR
R-1,2-PROPANEDIOL
HOH
water
MG
101
2
MG
MG
101
A
PGR
906
3
PGR
PGR
906
A
PGR
907
3
PGR
PGR
907
A
PGR
908
3
PGR
PGR
908
A
HOH
1
4
HOH
HOH
909
A
HOH
3
4
HOH
HOH
910
A
HOH
4
4
HOH
HOH
911
A
HOH
5
4
HOH
HOH
912
A
HOH
7
4
HOH
HOH
913
A
HOH
9
4
HOH
HOH
914
A
HOH
10
4
HOH
HOH
915
A
HOH
11
4
HOH
HOH
916
A
HOH
13
4
HOH
HOH
917
A
HOH
14
4
HOH
HOH
918
A
HOH
15
4
HOH
HOH
919
A
HOH
16
4
HOH
HOH
920
A
HOH
17
4
HOH
HOH
921
A
HOH
18
4
HOH
HOH
922
A
HOH
19
4
HOH
HOH
923
A
HOH
21
4
HOH
HOH
924
A
HOH
22
4
HOH
HOH
925
A
HOH
23
4
HOH
HOH
926
A
HOH
24
4
HOH
HOH
927
A
HOH
25
4
HOH
HOH
928
A
HOH
26
4
HOH
HOH
929
A
HOH
27
4
HOH
HOH
930
A
HOH
28
4
HOH
HOH
931
A
HOH
29
4
HOH
HOH
932
A
HOH
30
4
HOH
HOH
933
A
HOH
31
4
HOH
HOH
934
A
HOH
34
4
HOH
HOH
935
A
HOH
49
4
HOH
HOH
936
A
HOH
50
4
HOH
HOH
937
A
HOH
51
4
HOH
HOH
938
A
HOH
53
4
HOH
HOH
939
A
HOH
56
4
HOH
HOH
940
A
HOH
57
4
HOH
HOH
941
A
HOH
58
4
HOH
HOH
942
A
HOH
59
4
HOH
HOH
943
A
HOH
63
4
HOH
HOH
944
A
HOH
64
4
HOH
HOH
945
A
HOH
67
4
HOH
HOH
946
A
HOH
68
4
HOH
HOH
947
A
HOH
69
4
HOH
HOH
948
A
HOH
70
4
HOH
HOH
949
A
0.599
0.258
3.000
3.000
35.910
35.910
PRO
1
n
1
PRO
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
THR
4
n
4
THR
4
A
LEU
5
n
5
LEU
5
A
TRP
6
n
6
TRP
6
A
LYS
7
n
7
LYS
7
A
ARG
8
n
8
ARG
8
A
PRO
9
n
9
PRO
9
A
LEU
10
n
10
LEU
10
A
VAL
11
n
11
VAL
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
LYS
14
n
14
LYS
14
A
ILE
15
n
15
ILE
15
A
GLY
16
n
16
GLY
16
A
GLY
17
n
17
GLY
17
A
GLN
18
n
18
GLN
18
A
LEU
19
n
19
LEU
19
A
LYS
20
n
20
LYS
20
A
GLU
21
n
21
GLU
21
A
ALA
22
n
22
ALA
22
A
LEU
23
n
23
LEU
23
A
LEU
24
n
24
LEU
24
A
ASP
25
n
25
ASP
25
A
THR
26
n
26
THR
26
A
GLY
27
n
27
GLY
27
A
ALA
28
n
28
ALA
28
A
ASP
29
n
29
ASP
29
A
ASP
30
n
30
ASP
30
A
THR
31
n
31
THR
31
A
VAL
32
n
32
VAL
32
A
LEU
33
n
33
LEU
33
A
GLU
34
n
34
GLU
34
A
GLU
35
n
35
GLU
35
A
MET
36
n
36
MET
36
A
ASN
37
n
37
ASN
37
A
LEU
38
n
38
LEU
38
A
PRO
39
n
39
PRO
39
A
GLY
40
n
40
GLY
40
A
ARG
41
n
41
ARG
41
A
TRP
42
n
42
TRP
42
A
LYS
43
n
43
LYS
43
A
PRO
44
n
44
PRO
44
A
LYS
45
n
45
LYS
45
A
MET
46
n
46
MET
46
A
ILE
47
n
47
ILE
47
A
GLY
48
n
48
GLY
48
A
GLY
49
n
49
GLY
49
A
ILE
50
n
50
ILE
50
A
GLY
51
n
51
GLY
51
A
GLY
52
n
52
GLY
52
A
PHE
53
n
53
PHE
53
A
ILE
54
n
54
ILE
54
A
LYS
55
n
55
LYS
55
A
VAL
56
n
56
VAL
56
A
ARG
57
n
57
ARG
57
A
GLN
58
n
58
GLN
58
A
TYR
59
n
59
TYR
59
A
ASP
60
n
60
ASP
60
A
GLN
61
n
61
GLN
61
A
ILE
62
n
62
ILE
62
A
LEU
63
n
63
LEU
63
A
ILE
64
n
64
ILE
64
A
GLU
65
n
65
GLU
65
A
ILE
66
n
66
ILE
66
A
CYS
67
n
67
CYS
67
A
GLY
68
n
68
GLY
68
A
HIS
69
n
69
HIS
69
A
LYS
70
n
70
LYS
70
A
ALA
71
n
71
ALA
71
A
ILE
72
n
72
ILE
72
A
GLY
73
n
73
GLY
73
A
THR
74
n
74
THR
74
A
VAL
75
n
75
VAL
75
A
LEU
76
n
76
LEU
76
A
VAL
77
n
77
VAL
77
A
GLY
78
n
78
GLY
78
A
PRO
79
n
79
PRO
79
A
THR
80
n
80
THR
80
A
PRO
81
n
81
PRO
81
A
VAL
82
n
82
VAL
82
A
ASN
83
n
83
ASN
83
A
ILE
84
n
84
ILE
84
A
ILE
85
n
85
ILE
85
A
GLY
86
n
86
GLY
86
A
ARG
87
n
87
ARG
87
A
ASN
88
n
88
ASN
88
A
LEU
89
n
89
LEU
89
A
LEU
90
n
90
LEU
90
A
THR
91
n
91
THR
91
A
GLN
92
n
92
GLN
92
A
ILE
93
n
93
ILE
93
A
GLY
94
n
94
GLY
94
A
CYS
95
n
95
CYS
95
A
THR
96
n
96
THR
96
A
LEU
97
n
97
LEU
97
A
ASN
98
n
98
ASN
98
A
PHE
99
n
99
PHE
99
A
0.5841
-0.0234
-0.5132
0.4703
-0.0797
0.8671
-0.0603
0.0265
-0.0229
-0.1635
0.0850
-0.0834
0.0238
-0.1604
-0.0246
0.0118
-0.0227
0.0373
-0.0295
-0.0053
-0.0267
refined
5.3267
-5.2528
15.0909
X-RAY DIFFRACTION
A
1
A
1
A
99
A
99
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA,PQS
2
dimeric
4030
-6
10180
A
HOH
928
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
928
F
O
HOH
8_555
2.0
A
HOH
928
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
929
F
O
HOH
1_555
83.6
A
HOH
928
F
O
HOH
8_555
A
MG
101
B
MG
MG
1_555
A
HOH
929
F
O
HOH
1_555
84.6
A
HOH
928
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
929
F
O
HOH
8_555
79.3
A
HOH
928
F
O
HOH
8_555
A
MG
101
B
MG
MG
1_555
A
HOH
929
F
O
HOH
8_555
78.3
A
HOH
929
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
929
F
O
HOH
8_555
162.8
A
HOH
928
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
944
F
O
HOH
1_555
73.9
A
HOH
928
F
O
HOH
8_555
A
MG
101
B
MG
MG
1_555
A
HOH
944
F
O
HOH
1_555
72.0
A
HOH
929
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
944
F
O
HOH
1_555
100.2
A
HOH
929
F
O
HOH
8_555
A
MG
101
B
MG
MG
1_555
A
HOH
944
F
O
HOH
1_555
73.2
A
HOH
928
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
944
F
O
HOH
8_555
74.5
A
HOH
928
F
O
HOH
8_555
A
MG
101
B
MG
MG
1_555
A
HOH
944
F
O
HOH
8_555
76.4
A
HOH
929
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
944
F
O
HOH
8_555
79.7
A
HOH
929
F
O
HOH
8_555
A
MG
101
B
MG
MG
1_555
A
HOH
944
F
O
HOH
8_555
97.5
A
HOH
944
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
944
F
O
HOH
8_555
148.2
A
HOH
928
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
945
F
O
HOH
1_555
164.7
A
HOH
928
F
O
HOH
8_555
A
MG
101
B
MG
MG
1_555
A
HOH
945
F
O
HOH
1_555
165.7
A
HOH
929
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
945
F
O
HOH
1_555
81.2
A
HOH
929
F
O
HOH
8_555
A
MG
101
B
MG
MG
1_555
A
HOH
945
F
O
HOH
1_555
115.9
A
HOH
944
F
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
945
F
O
HOH
1_555
109.4
A
HOH
944
F
O
HOH
8_555
A
MG
101
B
MG
MG
1_555
A
HOH
945
F
O
HOH
1_555
102.0
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
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_555
-y,-x,-z+1/2
crystal symmetry operation
0.0000000000
0.0000000000
52.8100000000
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
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
GLN
18
A
O
GLN
18
A
N
ILE
15
A
N
ILE
15
A
N
LYS
14
A
N
LYS
14
A
O
GLU
65
A
O
GLU
65
1
A
MG
101
B
MG
1
A
HOH
928
F
HOH
1
A
CE
LYS
14
A
CE
LYS
14
0
Y
1
A
NZ
LYS
14
A
NZ
LYS
14
0
Y
1
A
CB
ARG
41
A
CB
ARG
41
0
Y
1
A
CG
ARG
41
A
CG
ARG
41
0
Y
1
A
CD
ARG
41
A
CD
ARG
41
0
Y
1
A
NE
ARG
41
A
NE
ARG
41
0
Y
1
A
CZ
ARG
41
A
CZ
ARG
41
0
Y
1
A
NH1
ARG
41
A
NH1
ARG
41
0
Y
1
A
NH2
ARG
41
A
NH2
ARG
41
0
Y
1
A
A
O
O
HOH
HOH
932
939
2.16
1
A
A
PRO
GLY
39
40
-143.44
1
9.03
1.50
119.30
128.33
A
A
A
C
N
CA
THR
PRO
PRO
80
81
81
Y
1
A
A
CA
CB
ARG
ARG
41
41
-0.191
0.022
1.535
1.344
N
1
A
GLU
34
-49.71
165.90
1
A
PRO
39
-65.48
-83.79
1
A
PRO
79
-78.09
48.47
protein_rep.param
water_rep.param
ion.param
38.072
0.80
0.00
0.00
0.80
0.00
-1.60
0.943
0.914
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.32073
0.23409
0.23834
2.15
44.46
393
7074
5.3
99.57
10.862
0.149
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.243
0.242
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
MASK
2.15
44.46
41
817
16
0
760
0.023
0.022
808
2.034
2.002
1096
10.260
5.000
104
44.988
25.172
29
17.117
15.000
146
17.376
15.000
4
0.168
0.200
130
0.008
0.020
588
0.235
0.200
291
0.313
0.200
538
0.211
0.200
41
0.327
0.200
56
0.191
0.200
8
2.540
1.500
527
3.539
2.000
824
5.677
3.000
323
7.613
4.500
272
0.529
0.378
2.206
26
500
20
98.87
2.150
44.440
2HB4
13572
13526
2.0
3.0
0.095
1.010
1
8.900
7.340
751
99.700
0.601
2.15
2.23
2.2
9663
1334
1.140
1
7.24
99.50
refinement
REFMAC
5.2.0005
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 reduction
CrystalClear
data scaling
Pflugrath, J.W.
jwp@RigakuMSC.com
Apr 27 2005
http://www.msc.com/protein/dtrek.html
d*TREK
package
9.4SSI
N
Structure of HIV Protease NL4-3 in an Unliganded State
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
4
N
N
A
GLY
86
A
GLY
86
HELX_P
A
THR
91
A
THR
91
1
1
6
metalc
2.317
A
MG
101
B
MG
MG
1_555
A
HOH
928
F
O
HOH
1_555
metalc
2.320
A
MG
101
B
MG
MG
1_555
A
HOH
928
F
O
HOH
8_555
metalc
2.106
A
MG
101
B
MG
MG
1_555
A
HOH
929
F
O
HOH
1_555
metalc
2.354
A
MG
101
B
MG
MG
1_555
A
HOH
929
F
O
HOH
8_555
metalc
2.782
A
MG
101
B
MG
MG
1_555
A
HOH
944
F
O
HOH
1_555
metalc
2.658
A
MG
101
B
MG
MG
1_555
A
HOH
944
F
O
HOH
8_555
metalc
3.082
A
MG
101
B
MG
MG
1_555
A
HOH
945
F
O
HOH
1_555
HYDROLASE
HIV, protease, aspartyl, retrovirus, HYDROLASE
POL_HV1BR
UNP
1
500
P03367
PQITLWRRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
500
598
2HB4
1
99
P03367
A
1
1
99
1
ARG
engineered mutation
LYS
7
2HB4
A
P03367
UNP
506
7
8
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
LYS
43
A
LYS
43
A
GLY
49
A
GLY
49
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
A
HIS
69
A
HIS
69
A
VAL
77
A
VAL
77
A
VAL
32
A
VAL
32
A
LEU
33
A
LEU
33
A
ILE
84
A
ILE
84
A
ILE
85
A
ILE
85
A
GLN
18
A
GLN
18
A
LEU
24
A
LEU
24
A
LEU
10
A
LEU
10
A
ILE
15
A
ILE
15
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
BINDING SITE FOR RESIDUE MG A 101
A
MG
101
Software
7
BINDING SITE FOR RESIDUE PGR A 906
A
PGR
906
Software
6
BINDING SITE FOR RESIDUE PGR A 907
A
PGR
907
Software
4
BINDING SITE FOR RESIDUE PGR A 908
A
PGR
908
Software
8
A
HOH
928
F
HOH
7
1_555
A
HOH
928
F
HOH
7
8_555
A
HOH
929
F
HOH
7
8_555
A
HOH
929
F
HOH
7
1_555
A
HOH
944
F
HOH
7
8_555
A
HOH
944
F
HOH
7
1_555
A
HOH
945
F
HOH
7
1_555
A
LYS
14
A
LYS
14
6
1_555
A
GLY
16
A
GLY
16
6
1_555
A
GLY
17
A
GLY
17
6
1_555
A
LEU
63
A
LEU
63
6
1_555
A
GLU
65
A
GLU
65
6
1_555
A
LYS
70
A
LYS
70
6
1_555
A
ASP
29
A
ASP
29
4
1_555
A
ASP
30
A
ASP
30
4
1_555
A
VAL
32
A
VAL
32
4
1_555
A
HOH
917
F
HOH
4
1_555
A
ILE
72
A
ILE
72
8
1_555
A
GLY
73
A
GLY
73
8
1_555
A
THR
74
A
THR
74
8
1_555
A
PRO
79
A
PRO
79
8
5_555
A
ASN
88
A
ASN
88
8
1_555
A
THR
91
A
THR
91
8
1_555
A
GLN
92
A
GLN
92
8
1_555
A
HOH
941
F
HOH
8
1_555
92
P 41 21 2