0.022284
0.000000
0.000000
0.000000
0.022284
0.000000
0.000000
0.000000
0.009491
0.00000
0.00000
0.00000
Yedidi, R.S.
Proteasa, G.
Kovari, L.C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
44.875
44.875
105.363
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
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
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
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
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
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
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
R
C
N
295
N
O
N
296
N
C
N
297
N
O
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
H
N
305
N
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
N
C
Y
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
N
Y
316
N
C
Y
317
N
C
Y
318
N
C
Y
319
N
C
Y
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
N
N
335
S
C
N
336
N
C
N
337
N
O
N
338
N
C
Y
339
N
C
Y
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
C
N
345
N
O
N
346
N
O
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
N
N
359
S
C
N
360
N
C
N
361
N
O
N
362
N
C
N
363
N
C
N
364
N
C
N
365
N
O
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
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
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
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
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
doub
N
267
N
sing
N
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
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
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
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
doub
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
Y
304
N
doub
Y
305
N
sing
Y
306
N
sing
N
307
N
sing
Y
308
N
doub
Y
309
N
sing
Y
310
N
sing
N
311
N
sing
Y
312
N
sing
Y
313
N
doub
N
314
N
sing
Y
315
N
doub
N
316
N
sing
Y
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
doub
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
Y
332
N
doub
Y
333
N
sing
Y
334
N
sing
N
335
N
sing
Y
336
N
doub
N
337
N
sing
Y
338
N
doub
N
339
N
sing
Y
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
doub
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
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
US
J.Mol.Graph.Model.
1093-3263
53C
105
111
10.1016/j.jmgm.2014.06.010
25108107
A multi-drug resistant HIV-1 protease is resistant to the dimerization inhibitory activity of TLF-PafF.
2014
10.2210/pdb4nkk/pdb
pdb_00004nkk
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
MAR CCD 165 mm
SINGLE WAVELENGTH
M
x-ray
1
0.99
1.0
5ID-B
APS
0.99
SYNCHROTRON
APS BEAMLINE 5ID-B
10725.582
HIV-1 protease
1
man
polymer
18.015
water
142
nat
water
no
no
PQITLWQRPVVTIKIGGQLKEALLNTGADDTVLEEVNLPGRWKPKLIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPT
PANVIGRNLMTQIGCTLNF
PQITLWQRPVVTIKIGGQLKEALLNTGADDTVLEEVNLPGRWKPKLIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPT
PANVIGRNLMTQIGCTLNF
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
sample
pol
11676
Human immunodeficiency virus 1
562
Escherichia coli
1
2.47
50.26
VAPOR DIFFUSION, HANGING DROP
7.3
0.3-1.0 M NaCl (precipitant), pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
repository
Initial release
Database references
Data collection
Database references
Refinement description
1
0
2014-07-09
1
1
2014-08-20
1
2
2023-09-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
Apo protease
Parent clinical isolate
RCSB
Y
RCSB
2013-11-12
REL
REL
HOH
water
THESEvARE CHARACTERISTIC MUTATIONS OF THE ORIGINAL PATIENT ISOLATE MDR769 HIV-1 PROTEASE
3PJ6
PDB
experimental model
HOH
1
2
HOH
HOH
101
A
HOH
2
2
HOH
HOH
102
A
HOH
3
2
HOH
HOH
103
A
HOH
4
2
HOH
HOH
104
A
HOH
5
2
HOH
HOH
105
A
HOH
6
2
HOH
HOH
106
A
HOH
7
2
HOH
HOH
107
A
HOH
8
2
HOH
HOH
108
A
HOH
9
2
HOH
HOH
109
A
HOH
10
2
HOH
HOH
110
A
HOH
11
2
HOH
HOH
111
A
HOH
12
2
HOH
HOH
112
A
HOH
13
2
HOH
HOH
113
A
HOH
14
2
HOH
HOH
114
A
HOH
15
2
HOH
HOH
115
A
HOH
16
2
HOH
HOH
116
A
HOH
17
2
HOH
HOH
117
A
HOH
18
2
HOH
HOH
118
A
HOH
19
2
HOH
HOH
119
A
HOH
20
2
HOH
HOH
120
A
HOH
21
2
HOH
HOH
121
A
HOH
22
2
HOH
HOH
122
A
HOH
23
2
HOH
HOH
123
A
HOH
24
2
HOH
HOH
124
A
HOH
25
2
HOH
HOH
125
A
HOH
26
2
HOH
HOH
126
A
HOH
27
2
HOH
HOH
127
A
HOH
28
2
HOH
HOH
128
A
HOH
29
2
HOH
HOH
129
A
HOH
30
2
HOH
HOH
130
A
HOH
31
2
HOH
HOH
131
A
HOH
32
2
HOH
HOH
132
A
HOH
33
2
HOH
HOH
133
A
HOH
34
2
HOH
HOH
134
A
HOH
35
2
HOH
HOH
135
A
HOH
36
2
HOH
HOH
136
A
HOH
37
2
HOH
HOH
137
A
HOH
38
2
HOH
HOH
138
A
HOH
39
2
HOH
HOH
139
A
HOH
40
2
HOH
HOH
140
A
HOH
41
2
HOH
HOH
141
A
HOH
42
2
HOH
HOH
142
A
HOH
43
2
HOH
HOH
143
A
HOH
44
2
HOH
HOH
144
A
HOH
45
2
HOH
HOH
145
A
HOH
46
2
HOH
HOH
146
A
HOH
47
2
HOH
HOH
147
A
HOH
48
2
HOH
HOH
148
A
HOH
49
2
HOH
HOH
149
A
HOH
50
2
HOH
HOH
150
A
HOH
51
2
HOH
HOH
151
A
HOH
52
2
HOH
HOH
152
A
HOH
53
2
HOH
HOH
153
A
HOH
54
2
HOH
HOH
154
A
HOH
55
2
HOH
HOH
155
A
HOH
56
2
HOH
HOH
156
A
HOH
57
2
HOH
HOH
157
A
HOH
58
2
HOH
HOH
158
A
HOH
59
2
HOH
HOH
159
A
HOH
60
2
HOH
HOH
160
A
HOH
61
2
HOH
HOH
161
A
HOH
62
2
HOH
HOH
162
A
HOH
63
2
HOH
HOH
163
A
HOH
64
2
HOH
HOH
164
A
HOH
65
2
HOH
HOH
165
A
HOH
66
2
HOH
HOH
166
A
HOH
67
2
HOH
HOH
167
A
HOH
68
2
HOH
HOH
168
A
HOH
69
2
HOH
HOH
169
A
HOH
70
2
HOH
HOH
170
A
HOH
71
2
HOH
HOH
171
A
HOH
72
2
HOH
HOH
172
A
HOH
73
2
HOH
HOH
173
A
HOH
74
2
HOH
HOH
174
A
HOH
75
2
HOH
HOH
175
A
HOH
76
2
HOH
HOH
176
A
HOH
77
2
HOH
HOH
177
A
HOH
78
2
HOH
HOH
178
A
HOH
79
2
HOH
HOH
179
A
HOH
80
2
HOH
HOH
180
A
HOH
81
2
HOH
HOH
181
A
HOH
82
2
HOH
HOH
182
A
HOH
83
2
HOH
HOH
183
A
HOH
84
2
HOH
HOH
184
A
HOH
85
2
HOH
HOH
185
A
HOH
86
2
HOH
HOH
186
A
HOH
87
2
HOH
HOH
187
A
HOH
88
2
HOH
HOH
188
A
HOH
89
2
HOH
HOH
189
A
HOH
90
2
HOH
HOH
190
A
HOH
91
2
HOH
HOH
191
A
HOH
92
2
HOH
HOH
192
A
HOH
93
2
HOH
HOH
193
A
HOH
94
2
HOH
HOH
194
A
HOH
95
2
HOH
HOH
195
A
HOH
96
2
HOH
HOH
196
A
HOH
97
2
HOH
HOH
197
A
HOH
98
2
HOH
HOH
198
A
HOH
99
2
HOH
HOH
199
A
HOH
100
2
HOH
HOH
200
A
HOH
101
2
HOH
HOH
201
A
HOH
102
2
HOH
HOH
202
A
HOH
103
2
HOH
HOH
203
A
HOH
104
2
HOH
HOH
204
A
HOH
105
2
HOH
HOH
205
A
HOH
106
2
HOH
HOH
206
A
HOH
107
2
HOH
HOH
207
A
HOH
108
2
HOH
HOH
208
A
HOH
109
2
HOH
HOH
209
A
HOH
110
2
HOH
HOH
210
A
HOH
111
2
HOH
HOH
211
A
HOH
112
2
HOH
HOH
212
A
HOH
113
2
HOH
HOH
213
A
HOH
114
2
HOH
HOH
214
A
HOH
115
2
HOH
HOH
215
A
HOH
116
2
HOH
HOH
216
A
HOH
117
2
HOH
HOH
217
A
HOH
118
2
HOH
HOH
218
A
HOH
119
2
HOH
HOH
219
A
HOH
120
2
HOH
HOH
220
A
HOH
121
2
HOH
HOH
221
A
HOH
122
2
HOH
HOH
222
A
HOH
123
2
HOH
HOH
223
A
HOH
124
2
HOH
HOH
224
A
HOH
125
2
HOH
HOH
225
A
HOH
126
2
HOH
HOH
226
A
HOH
127
2
HOH
HOH
227
A
HOH
128
2
HOH
HOH
228
A
HOH
129
2
HOH
HOH
229
A
HOH
130
2
HOH
HOH
230
A
HOH
131
2
HOH
HOH
231
A
HOH
132
2
HOH
HOH
232
A
HOH
133
2
HOH
HOH
233
A
HOH
134
2
HOH
HOH
234
A
HOH
135
2
HOH
HOH
235
A
HOH
136
2
HOH
HOH
236
A
HOH
137
2
HOH
HOH
237
A
HOH
138
2
HOH
HOH
238
A
HOH
139
2
HOH
HOH
239
A
HOH
140
2
HOH
HOH
240
A
HOH
141
2
HOH
HOH
241
A
HOH
142
2
HOH
HOH
242
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
GLN
7
n
7
GLN
7
A
ARG
8
n
8
ARG
8
A
PRO
9
n
9
PRO
9
A
VAL
10
n
10
VAL
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
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
VAL
36
n
36
VAL
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
LEU
46
n
46
LEU
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
VAL
54
n
54
VAL
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
VAL
62
n
62
VAL
62
A
PRO
63
n
63
PRO
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
VAL
71
n
71
VAL
71
A
ILE
72
n
72
ILE
72
A
GLY
73
n
73
GLY
73
A
THR
74
n
74
THR
74
A
VAL
75
n
75
VAL
75
A
LEU
76
n
76
LEU
76
A
VAL
77
n
77
VAL
77
A
GLY
78
n
78
GLY
78
A
PRO
79
n
79
PRO
79
A
THR
80
n
80
THR
80
A
PRO
81
n
81
PRO
81
A
ALA
82
n
82
ALA
82
A
ASN
83
n
83
ASN
83
A
VAL
84
n
84
VAL
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
MET
90
n
90
MET
90
A
THR
91
n
91
THR
91
A
GLN
92
n
92
GLN
92
A
ILE
93
n
93
ILE
93
A
GLY
94
n
94
GLY
94
A
CYS
95
n
95
CYS
95
A
THR
96
n
96
THR
96
A
LEU
97
n
97
LEU
97
A
ASN
98
n
98
ASN
98
A
PHE
99
n
99
PHE
99
A
author_and_software_defined_assembly
PISA
2
dimeric
2940
-18
10620
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
7_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
N
LYS
45
A
N
LYS
45
A
O
VAL
56
A
O
VAL
56
A
N
ILE
64
A
N
ILE
64
A
O
VAL
71
A
O
VAL
71
A
O
LEU
76
A
O
LEU
76
A
N
LEU
33
A
N
LEU
33
A
N
VAL
32
A
N
VAL
32
A
O
VAL
84
A
O
VAL
84
A
O
ILE
85
A
O
ILE
85
A
N
LEU
23
A
N
LEU
23
A
O
ALA
22
A
O
ALA
22
A
N
VAL
11
A
N
VAL
11
A
N
LYS
14
A
N
LYS
14
A
O
GLU
65
A
O
GLU
65
1
A
HOH
219
B
HOH
1
A
CB
GLU
35
A
CB
GLU
35
0
Y
1
A
A
NZ
O
LYS
HOH
55
203
2.07
1
A
A
O
O
HOH
HOH
158
191
2.09
1
A
A
O
O
HOH
HOH
158
195
2.15
1
A
A
NZ
O
LYS
HOH
43
227
2.16
1
A
A
O
O
THR
HOH
80
202
2.16
1
A
A
O
O
HOH
HOH
113
207
1.77
1_555
3_455
1
A
A
O
O
HOH
HOH
128
181
1.87
1_555
6_444
1
A
A
O
O
HOH
HOH
181
190
2.16
1_555
6_544
0.2491
0.2039
0.2061
1.800
26.341
537
10575
5.08
99.91
0.15
1
1.34
MOLECULAR REPLACEMENT
23.13
0.90
1.11
3PJ6
ML
FLAT BULK SOLVENT MODEL
1.800
26.341
142
895
0
0
753
0.007
767
1.113
1043
13.423
286
0.069
125
0.006
132
0.2720
0.2156
1.9811
147
2412
100.00
0.2623
0.2056
2.2676
132
2474
100.00
0.2682
0.2231
2.8564
129
2492
100.00
0.2284
0.1909
26.3436
129
2660
100.00
1.56
35.11
4NKK
0.06
1
data collection
HKL-2000
phasing
MOLREP
refinement
PHENIX
(phenix.refine: 1.8.2_1309)
data reduction
MOSFLM
data scaling
SCALA
Crystal structure of a multi-drug resistant clinical isolate-769 HIV-1 protease variant that is resistant to the dimerization inhibitory activity of TLF-PafF
1
N
N
2
N
N
A
GLY
86
A
GLY
86
HELX_P
A
GLY
94
A
GLY
94
1
1
9
HYDROLASE
HIV, AIDS, HIV-1 protease, dimerization inhibitors, protease inhibitors, multidrug-resistance, clinical isolate 769, dimer protease, Hydrolase
Q000H7_9HIV1
UNP
1
1
Q000H7
PQITLWQRPIVTIKIGGQLKEALLDTGADDTVLEDINLPGRWKPKMIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPT
PTNVIGRNLMTQIGCTLNF
1
99
4NKK
1
99
Q000H7
A
1
1
99
1
ILE
engineered mutation
VAL
10
4NKK
A
Q000H7
UNP
10
10
1
ASP
engineered mutation
ASN
25
4NKK
A
Q000H7
UNP
25
25
1
ASP
SEE REMARK 999
GLU
35
4NKK
A
Q000H7
UNP
35
35
1
ILE
SEE REMARK 999
VAL
36
4NKK
A
Q000H7
UNP
36
36
1
MET
SEE REMARK 999
LEU
46
4NKK
A
Q000H7
UNP
46
46
1
THR
SEE REMARK 999
ALA
82
4NKK
A
Q000H7
UNP
82
82
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
VAL
84
A
VAL
84
A
ILE
85
A
ILE
85
A
GLN
18
A
GLN
18
A
LEU
24
A
LEU
24
A
VAL
10
A
VAL
10
A
ILE
15
A
ILE
15
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
92
P 41 21 2