0.010822
0.006248
0.000000
0.000000
0.012496
0.000000
0.000000
0.000000
0.017389
0.000000
0.000000
0.000000
Gres, A.T.
Kirby, K.A.
Sarafianos, S.G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.000
90.000
120.000
92.407
92.407
57.509
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
Cl -1
35.453
CHLORIDE ION
non-polymer
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
I -1
126.904
IODIDE ION
non-polymer
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
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
CL
N
75
N
N
N
76
R
C
N
77
N
C
N
78
N
O
N
79
N
C
N
80
N
S
N
81
N
O
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
N
N
90
S
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
C
N
95
N
C
N
96
N
O
N
97
N
N
N
98
N
O
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
N
N
110
S
C
N
111
N
C
N
112
N
O
N
113
N
C
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
O
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
N
N
129
N
C
N
130
N
C
N
131
N
O
N
132
N
O
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
N
N
139
S
C
N
140
N
C
N
141
N
O
N
142
N
C
Y
143
N
C
Y
144
N
N
Y
145
N
C
Y
146
N
C
Y
147
N
N
N
148
N
O
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
H
N
159
N
O
N
160
N
H
N
161
N
H
N
162
N
N
N
163
S
C
N
164
N
C
N
165
N
O
N
166
S
C
N
167
N
C
N
168
N
C
N
169
N
C
N
170
N
O
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
H
N
184
N
I
N
185
N
N
N
186
S
C
N
187
N
C
N
188
N
O
N
189
N
C
N
190
N
C
N
191
N
C
N
192
N
C
N
193
N
O
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
H
N
206
N
H
N
207
N
N
N
208
S
C
N
209
N
C
N
210
N
O
N
211
N
C
N
212
N
C
N
213
N
C
N
214
N
C
N
215
N
N
N
216
N
O
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
H
N
231
N
H
N
232
N
N
N
233
S
C
N
234
N
C
N
235
N
O
N
236
N
C
N
237
N
C
N
238
N
S
N
239
N
C
N
240
N
O
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
H
N
251
N
H
N
252
N
N
N
253
S
C
N
254
N
C
N
255
N
O
N
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
Y
262
N
C
N
263
N
O
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
H
N
274
N
H
N
275
N
N
N
276
S
C
N
277
N
C
N
278
N
O
N
279
N
C
N
280
N
C
N
281
N
C
N
282
N
O
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
H
N
291
N
H
N
292
N
N
N
293
S
C
N
294
N
C
N
295
N
O
N
296
N
C
N
297
N
O
N
298
N
O
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
N
N
307
S
C
N
308
N
C
N
309
N
O
N
310
R
C
N
311
N
O
N
312
N
C
N
313
N
O
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
H
N
322
N
H
N
323
N
N
N
324
S
C
N
325
N
C
N
326
N
O
N
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
N
Y
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
C
Y
336
N
C
N
337
N
O
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
H
N
349
N
H
N
350
N
N
N
351
S
C
N
352
N
C
N
353
N
O
N
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
C
Y
360
N
C
N
361
N
O
N
362
N
O
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
H
N
373
N
H
N
374
N
N
N
375
S
C
N
376
N
C
N
377
N
O
N
378
N
C
N
379
N
C
N
380
N
C
N
381
N
O
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
391
N
H
N
392
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
doub
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
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
sing
N
340
N
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
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
sing
N
364
N
doub
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
To be published
0353
Identification of a novel element in HIV-1 capsid critical for assembly and maturation
10.2210/pdb6axt/pdb
pdb_00006axt
100
1
CCD
2015-11-08
MARMOSAIC 300 mm CCD
SINGLE WAVELENGTH
M
x-ray
1
1.033760
1.0
23-ID-B
APS
1.033760
SYNCHROTRON
APS BEAMLINE 23-ID-B
25602.416
HIV-1 capsid protein
UNP residues 133-363
T58S, T107I, P122A
1
man
polymer
126.904
IODIDE ION
9
syn
non-polymer
35.453
CHLORIDE ION
6
syn
non-polymer
18.015
water
41
nat
water
no
no
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNSVGGHQAAMQMLKETINEEAAEW
DRLHPVHAGPIAPGQMREPRGSDIAGITSTLQEQIGWMTHNAPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEP
FRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNSVGGHQAAMQMLKETINEEAAEW
DRLHPVHAGPIAPGQMREPRGSDIAGITSTLQEQIGWMTHNAPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEP
FRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL
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
n
n
n
n
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
1
231
gag
11676
Human immunodeficiency virus 1
469008
Escherichia coli
BL21(DE3)
plasmid
Biological sequence
pET11a
1
2.77
55.57
0.210
VAPOR DIFFUSION, HANGING DROP
PEG3350, NaI, MIB, Glycerol
291
pdbx_audit_support
pdbx_audit_support
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Author supporting evidence
Data collection
Author supporting evidence
Data collection
Database references
Refinement description
1
0
2018-09-12
1
1
2019-02-20
1
2
2019-12-11
1
3
2023-10-04
_pdbx_audit_support.funding_organization
_pdbx_audit_support.funding_organization
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
AI120860
Structure of the native full-length HIV-1 capsid protein
P122A mutant of the HIV-1 capsid protein
V11I/T58A/P122A mutant of the HIV-1 capsid protein
N
RCSB
Y
RCSB
2017-09-07
REL
REL
IOD
IODIDE ION
CL
CHLORIDE ION
HOH
water
4XFX
PDB
experimental model
IOD
301
2
IOD
IOD
301
A
IOD
302
2
IOD
IOD
302
A
IOD
303
2
IOD
IOD
303
A
IOD
304
2
IOD
IOD
304
A
IOD
305
2
IOD
IOD
305
A
IOD
306
2
IOD
IOD
306
A
IOD
307
2
IOD
IOD
307
A
IOD
308
2
IOD
IOD
308
A
IOD
309
2
IOD
IOD
309
A
CL
310
3
CL
CL
310
A
CL
311
3
CL
CL
311
A
CL
312
3
CL
CL
312
A
CL
313
3
CL
CL
313
A
CL
314
3
CL
CL
314
A
CL
315
3
CL
CL
315
A
HOH
435
4
HOH
HOH
401
A
HOH
423
4
HOH
HOH
402
A
HOH
420
4
HOH
HOH
403
A
HOH
429
4
HOH
HOH
404
A
HOH
406
4
HOH
HOH
405
A
HOH
438
4
HOH
HOH
406
A
HOH
437
4
HOH
HOH
407
A
HOH
412
4
HOH
HOH
408
A
HOH
432
4
HOH
HOH
409
A
HOH
417
4
HOH
HOH
410
A
HOH
402
4
HOH
HOH
411
A
HOH
414
4
HOH
HOH
412
A
HOH
430
4
HOH
HOH
413
A
HOH
411
4
HOH
HOH
414
A
HOH
433
4
HOH
HOH
415
A
HOH
416
4
HOH
HOH
416
A
HOH
403
4
HOH
HOH
417
A
HOH
441
4
HOH
HOH
418
A
HOH
407
4
HOH
HOH
419
A
HOH
424
4
HOH
HOH
420
A
HOH
409
4
HOH
HOH
421
A
HOH
410
4
HOH
HOH
422
A
HOH
422
4
HOH
HOH
423
A
HOH
401
4
HOH
HOH
424
A
HOH
440
4
HOH
HOH
425
A
HOH
434
4
HOH
HOH
426
A
HOH
425
4
HOH
HOH
427
A
HOH
413
4
HOH
HOH
428
A
HOH
436
4
HOH
HOH
429
A
HOH
408
4
HOH
HOH
430
A
HOH
418
4
HOH
HOH
431
A
HOH
404
4
HOH
HOH
432
A
HOH
431
4
HOH
HOH
433
A
HOH
421
4
HOH
HOH
434
A
HOH
405
4
HOH
HOH
435
A
HOH
415
4
HOH
HOH
436
A
HOH
439
4
HOH
HOH
437
A
HOH
419
4
HOH
HOH
438
A
HOH
428
4
HOH
HOH
439
A
HOH
427
4
HOH
HOH
440
A
HOH
426
4
HOH
HOH
441
A
2.400
2.400
46.700
46.700
Phaser MODE: MR_AUTO
PRO
1
n
1
PRO
1
A
ILE
2
n
2
ILE
2
A
VAL
3
n
3
VAL
3
A
GLN
4
n
4
GLN
4
A
n
5
5
A
n
6
6
A
n
7
7
A
n
8
8
A
GLN
9
n
9
GLN
9
A
MET
10
n
10
MET
10
A
VAL
11
n
11
VAL
11
A
HIS
12
n
12
HIS
12
A
GLN
13
n
13
GLN
13
A
ALA
14
n
14
ALA
14
A
ILE
15
n
15
ILE
15
A
SER
16
n
16
SER
16
A
PRO
17
n
17
PRO
17
A
ARG
18
n
18
ARG
18
A
THR
19
n
19
THR
19
A
LEU
20
n
20
LEU
20
A
ASN
21
n
21
ASN
21
A
ALA
22
n
22
ALA
22
A
TRP
23
n
23
TRP
23
A
VAL
24
n
24
VAL
24
A
LYS
25
n
25
LYS
25
A
VAL
26
n
26
VAL
26
A
VAL
27
n
27
VAL
27
A
GLU
28
n
28
GLU
28
A
GLU
29
n
29
GLU
29
A
LYS
30
n
30
LYS
30
A
ALA
31
n
31
ALA
31
A
PHE
32
n
32
PHE
32
A
SER
33
n
33
SER
33
A
PRO
34
n
34
PRO
34
A
GLU
35
n
35
GLU
35
A
VAL
36
n
36
VAL
36
A
ILE
37
n
37
ILE
37
A
PRO
38
n
38
PRO
38
A
MET
39
n
39
MET
39
A
PHE
40
n
40
PHE
40
A
SER
41
n
41
SER
41
A
ALA
42
n
42
ALA
42
A
LEU
43
n
43
LEU
43
A
SER
44
n
44
SER
44
A
GLU
45
n
45
GLU
45
A
GLY
46
n
46
GLY
46
A
ALA
47
n
47
ALA
47
A
THR
48
n
48
THR
48
A
PRO
49
n
49
PRO
49
A
GLN
50
n
50
GLN
50
A
ASP
51
n
51
ASP
51
A
LEU
52
n
52
LEU
52
A
ASN
53
n
53
ASN
53
A
THR
54
n
54
THR
54
A
MET
55
n
55
MET
55
A
LEU
56
n
56
LEU
56
A
ASN
57
n
57
ASN
57
A
SER
58
n
58
SER
58
A
VAL
59
n
59
VAL
59
A
GLY
60
n
60
GLY
60
A
GLY
61
n
61
GLY
61
A
HIS
62
n
62
HIS
62
A
GLN
63
n
63
GLN
63
A
ALA
64
n
64
ALA
64
A
ALA
65
n
65
ALA
65
A
MET
66
n
66
MET
66
A
GLN
67
n
67
GLN
67
A
MET
68
n
68
MET
68
A
LEU
69
n
69
LEU
69
A
LYS
70
n
70
LYS
70
A
GLU
71
n
71
GLU
71
A
THR
72
n
72
THR
72
A
ILE
73
n
73
ILE
73
A
ASN
74
n
74
ASN
74
A
GLU
75
n
75
GLU
75
A
GLU
76
n
76
GLU
76
A
ALA
77
n
77
ALA
77
A
ALA
78
n
78
ALA
78
A
GLU
79
n
79
GLU
79
A
TRP
80
n
80
TRP
80
A
ASP
81
n
81
ASP
81
A
ARG
82
n
82
ARG
82
A
LEU
83
n
83
LEU
83
A
HIS
84
n
84
HIS
84
A
PRO
85
n
85
PRO
85
A
VAL
86
n
86
VAL
86
A
HIS
87
n
87
HIS
87
A
ALA
88
n
88
ALA
88
A
GLY
89
n
89
GLY
89
A
PRO
90
n
90
PRO
90
A
ILE
91
n
91
ILE
91
A
ALA
92
n
92
ALA
92
A
PRO
93
n
93
PRO
93
A
GLY
94
n
94
GLY
94
A
GLN
95
n
95
GLN
95
A
MET
96
n
96
MET
96
A
ARG
97
n
97
ARG
97
A
GLU
98
n
98
GLU
98
A
PRO
99
n
99
PRO
99
A
ARG
100
n
100
ARG
100
A
GLY
101
n
101
GLY
101
A
SER
102
n
102
SER
102
A
ASP
103
n
103
ASP
103
A
ILE
104
n
104
ILE
104
A
ALA
105
n
105
ALA
105
A
GLY
106
n
106
GLY
106
A
ILE
107
n
107
ILE
107
A
THR
108
n
108
THR
108
A
SER
109
n
109
SER
109
A
THR
110
n
110
THR
110
A
LEU
111
n
111
LEU
111
A
GLN
112
n
112
GLN
112
A
GLU
113
n
113
GLU
113
A
GLN
114
n
114
GLN
114
A
ILE
115
n
115
ILE
115
A
GLY
116
n
116
GLY
116
A
TRP
117
n
117
TRP
117
A
MET
118
n
118
MET
118
A
THR
119
n
119
THR
119
A
HIS
120
n
120
HIS
120
A
ASN
121
n
121
ASN
121
A
ALA
122
n
122
ALA
122
A
PRO
123
n
123
PRO
123
A
ILE
124
n
124
ILE
124
A
PRO
125
n
125
PRO
125
A
VAL
126
n
126
VAL
126
A
GLY
127
n
127
GLY
127
A
GLU
128
n
128
GLU
128
A
ILE
129
n
129
ILE
129
A
TYR
130
n
130
TYR
130
A
LYS
131
n
131
LYS
131
A
ARG
132
n
132
ARG
132
A
TRP
133
n
133
TRP
133
A
ILE
134
n
134
ILE
134
A
ILE
135
n
135
ILE
135
A
LEU
136
n
136
LEU
136
A
GLY
137
n
137
GLY
137
A
LEU
138
n
138
LEU
138
A
ASN
139
n
139
ASN
139
A
LYS
140
n
140
LYS
140
A
ILE
141
n
141
ILE
141
A
VAL
142
n
142
VAL
142
A
ARG
143
n
143
ARG
143
A
MET
144
n
144
MET
144
A
TYR
145
n
145
TYR
145
A
SER
146
n
146
SER
146
A
PRO
147
n
147
PRO
147
A
THR
148
n
148
THR
148
A
SER
149
n
149
SER
149
A
ILE
150
n
150
ILE
150
A
LEU
151
n
151
LEU
151
A
ASP
152
n
152
ASP
152
A
ILE
153
n
153
ILE
153
A
ARG
154
n
154
ARG
154
A
GLN
155
n
155
GLN
155
A
GLY
156
n
156
GLY
156
A
PRO
157
n
157
PRO
157
A
LYS
158
n
158
LYS
158
A
GLU
159
n
159
GLU
159
A
PRO
160
n
160
PRO
160
A
PHE
161
n
161
PHE
161
A
ARG
162
n
162
ARG
162
A
ASP
163
n
163
ASP
163
A
TYR
164
n
164
TYR
164
A
VAL
165
n
165
VAL
165
A
ASP
166
n
166
ASP
166
A
ARG
167
n
167
ARG
167
A
PHE
168
n
168
PHE
168
A
TYR
169
n
169
TYR
169
A
LYS
170
n
170
LYS
170
A
THR
171
n
171
THR
171
A
LEU
172
n
172
LEU
172
A
ARG
173
n
173
ARG
173
A
ALA
174
n
174
ALA
174
A
GLU
175
n
175
GLU
175
A
GLN
176
n
176
GLN
176
A
ALA
177
n
177
ALA
177
A
SER
178
n
178
SER
178
A
GLN
179
n
179
GLN
179
A
GLU
180
n
180
GLU
180
A
VAL
181
n
181
VAL
181
A
LYS
182
n
182
LYS
182
A
ASN
183
n
183
ASN
183
A
TRP
184
n
184
TRP
184
A
MET
185
n
185
MET
185
A
THR
186
n
186
THR
186
A
GLU
187
n
187
GLU
187
A
THR
188
n
188
THR
188
A
LEU
189
n
189
LEU
189
A
LEU
190
n
190
LEU
190
A
VAL
191
n
191
VAL
191
A
GLN
192
n
192
GLN
192
A
ASN
193
n
193
ASN
193
A
ALA
194
n
194
ALA
194
A
ASN
195
n
195
ASN
195
A
PRO
196
n
196
PRO
196
A
ASP
197
n
197
ASP
197
A
CYS
198
n
198
CYS
198
A
LYS
199
n
199
LYS
199
A
THR
200
n
200
THR
200
A
ILE
201
n
201
ILE
201
A
LEU
202
n
202
LEU
202
A
LYS
203
n
203
LYS
203
A
ALA
204
n
204
ALA
204
A
LEU
205
n
205
LEU
205
A
GLY
206
n
206
GLY
206
A
PRO
207
n
207
PRO
207
A
GLY
208
n
208
GLY
208
A
ALA
209
n
209
ALA
209
A
THR
210
n
210
THR
210
A
LEU
211
n
211
LEU
211
A
GLU
212
n
212
GLU
212
A
GLU
213
n
213
GLU
213
A
MET
214
n
214
MET
214
A
MET
215
n
215
MET
215
A
THR
216
n
216
THR
216
A
ALA
217
n
217
ALA
217
A
CYS
218
n
218
CYS
218
A
GLN
219
n
219
GLN
219
A
GLY
220
n
220
GLY
220
A
VAL
221
n
221
VAL
221
A
n
222
222
A
n
223
223
A
n
224
224
A
n
225
225
A
n
226
226
A
n
227
227
A
n
228
228
A
n
229
229
A
n
230
230
A
n
231
231
A
0.1286
0.2966
0.0825
0.1409
-0.3105
-0.0077
1.9205
-0.7484
-0.7953
2.3307
1.2100
2.1615
-0.8441
-0.4647
0.0070
1.4003
0.0968
0.0211
0.8926
0.0869
0.9478
refined
-1.5768
-12.3696
15.2179
X-RAY DIFFRACTION
0.5819
-0.7765
0.2860
0.2579
0.5844
1.0173
-0.1660
0.7247
0.8323
-0.0214
-0.0268
-0.2850
-0.7533
0.0146
-0.0001
0.5363
-0.0047
-0.0356
0.7492
0.1185
0.8585
refined
2.8479
-17.0688
-3.4882
X-RAY DIFFRACTION
1.2666
-0.4759
-0.3262
2.2620
-0.0058
1.9868
-0.2256
0.0686
0.1707
0.4640
-0.1787
-0.1673
0.4836
-0.0468
0.0001
0.4866
-0.0200
0.0673
0.4218
0.0409
0.4868
refined
-3.5287
-29.5493
3.2584
X-RAY DIFFRACTION
-0.1651
0.2833
-0.4170
-0.0854
0.0269
1.7600
0.0020
-0.3633
-0.4782
0.5642
-0.1254
0.1524
-0.6407
-0.1525
0.0000
1.0798
-0.0708
0.0004
0.6757
0.0139
0.6014
refined
-6.7039
-29.4263
20.5225
X-RAY DIFFRACTION
1.4047
-0.4302
-0.9952
0.9510
1.6793
1.9562
-0.1934
0.5552
-0.3343
-0.1698
-0.1041
0.0529
0.0079
-0.4557
-0.0001
0.5068
0.0447
-0.0036
0.5878
0.1442
0.5748
refined
14.3696
-28.0746
-8.9530
X-RAY DIFFRACTION
0.0229
0.3111
-0.0901
1.0978
-0.0615
0.2542
0.3460
-0.3621
1.2063
0.4299
-0.0709
-0.2456
0.7669
0.7160
0.0004
0.6276
0.1569
-0.0194
0.7175
0.0851
0.7175
refined
24.3490
-34.6305
-6.9274
X-RAY DIFFRACTION
0.9638
0.0422
-1.4779
1.1527
-0.2224
0.7817
-0.3022
0.0237
0.2965
-0.5845
-0.0636
-0.2145
0.4146
1.7209
-0.0012
0.6365
0.1824
0.0699
1.0360
0.1167
0.6502
refined
35.7375
-25.3444
-15.0095
X-RAY DIFFRACTION
A
1
A
16
X-RAY DIFFRACTION
1
chain 'A' and (resid 1 through 16 )
A
17
A
44
X-RAY DIFFRACTION
2
chain 'A' and (resid 17 through 44 )
A
45
A
83
X-RAY DIFFRACTION
3
chain 'A' and (resid 45 through 83 )
A
84
A
125
X-RAY DIFFRACTION
4
chain 'A' and (resid 84 through 125 )
A
126
A
174
X-RAY DIFFRACTION
5
chain 'A' and (resid 126 through 174 )
A
175
A
192
X-RAY DIFFRACTION
6
chain 'A' and (resid 175 through 192 )
A
193
A
221
X-RAY DIFFRACTION
7
chain 'A' and (resid 193 through 221 )
author_and_software_defined_assembly
PISA
6
hexameric
none
29720
-471
58760
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
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_555
-y,x-y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_555
-x+y,-x,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
4_555
-x,-y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.5000000000
0.8660254038
0.0000000000
-0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
5_555
y,-x+y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.5000000000
-0.8660254038
0.0000000000
0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
6_555
x-y,x,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
N
VAL
3
A
N
VAL
3
A
O
VAL
11
A
O
VAL
11
1
A
CG
GLN
9
A
CG
GLN
9
1
Y
1
A
CD
GLN
9
A
CD
GLN
9
1
Y
1
A
OE1
GLN
9
A
OE1
GLN
9
1
Y
1
A
NE2
GLN
9
A
NE2
GLN
9
1
Y
1
A
ASN
5
A
ASN
5
1
Y
1
A
LEU
6
A
LEU
6
1
Y
1
A
GLN
7
A
GLN
7
1
Y
1
A
GLY
8
A
GLY
8
1
Y
1
A
GLY
222
A
GLY
222
1
Y
1
A
GLY
223
A
GLY
223
1
Y
1
A
PRO
224
A
PRO
224
1
Y
1
A
GLY
225
A
GLY
225
1
Y
1
A
HIS
226
A
HIS
226
1
Y
1
A
LYS
227
A
LYS
227
1
Y
1
A
ALA
228
A
ALA
228
1
Y
1
A
ARG
229
A
ARG
229
1
Y
1
A
VAL
230
A
VAL
230
1
Y
1
A
LEU
231
A
LEU
231
1
Y
1
A
ALA
31
54.95
-105.46
174.510
79.5318
37.800
0.2433
0.2237
0.2247
2.4000
46.700
500
10446
4.7900
94.1500
0.3000
1
FREE R-VALUE
1.350
MOLECULAR REPLACEMENT
31.5500
0.9000
1.1100
4XFX
2.4000
46.700
41
1746
92.03
67.19
15
0
1690
217
0.002
1732
0.474
2354
0.038
264
0.004
305
9.193
1066
0.3296
0.0000
0.3011
2.6419
131
2505
2636
4
96.0000
0.3136
0.0000
0.2911
3.0241
104
2519
2623
4
95.0000
0.2508
0.0000
0.2433
3.8098
124
2465
2589
4
94.0000
0.2194
0.0000
0.1898
46.7099
141
2457
2598
4
92.0000
60.440
2.400
46.700
6AXT
10448
0.999
0.071
0.026
0.075
1
17.700
86620
8.300
0
94.100
1.313
2.400
2.490
1099
0.490
0.490
1.406
1
8.100
95.200
0.042
8.980
46.700
205
0.998
0.016
0.046
1
7.600
88.900
data scaling
Aimless
0.5.17
data collection
Blu-Ice
refinement
PHENIX
1.11.1-2575_1692
data extraction
PDB_EXTRACT
3.22
data reduction
Aimless
0.5.17
phasing
PHASER
2.5.7
N
Structure of the T58S/T107I/P122A mutant of the HIV-1 capsid protein
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
4
N
N
A
SER
16
A
SER
16
HELX_P
A
ALA
31
A
ALA
31
1
AA1
16
A
GLU
35
A
GLU
35
HELX_P
A
SER
44
A
SER
44
1
AA2
10
A
THR
48
A
THR
48
HELX_P
A
SER
58
A
SER
58
1
AA3
11
A
HIS
62
A
HIS
62
HELX_P
A
HIS
84
A
HIS
84
1
AA4
23
A
ARG
100
A
ARG
100
HELX_P
A
ALA
105
A
ALA
105
1
AA5
6
A
THR
110
A
THR
110
HELX_P
A
HIS
120
A
HIS
120
1
AA6
11
A
PRO
125
A
PRO
125
HELX_P
A
TYR
145
A
TYR
145
1
AA7
21
A
SER
149
A
SER
149
HELX_P
A
ILE
153
A
ILE
153
5
AA8
5
A
PRO
160
A
PRO
160
HELX_P
A
GLU
175
A
GLU
175
1
AA9
16
A
SER
178
A
SER
178
HELX_P
A
ASN
193
A
ASN
193
1
AB1
16
A
ASN
195
A
ASN
195
HELX_P
A
ALA
204
A
ALA
204
1
AB2
10
A
THR
210
A
THR
210
HELX_P
A
GLN
219
A
GLN
219
1
AB3
10
disulf
2.037
A
A
CYS
198
A
SG
CYS
198
1_555
A
CYS
218
A
SG
CYS
218
1_555
VIRAL PROTEIN
HIV-1 capsid protein, hexamer, T58S/T107I/P122A mutant, VIRAL PROTEIN
B6DRA0_9HIV1
UNP
1
133
B6DRA0
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEW
DRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEP
FRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL
133
363
6AXT
1
231
B6DRA0
A
1
1
231
1
THR
engineered mutation
SER
58
6AXT
A
B6DRA0
UNP
190
58
1
THR
engineered mutation
ILE
107
6AXT
A
B6DRA0
UNP
239
107
1
PRO
engineered mutation
ALA
122
6AXT
A
B6DRA0
UNP
254
122
2
anti-parallel
A
ILE
2
A
ILE
2
A
VAL
3
A
VAL
3
A
VAL
11
A
VAL
11
A
HIS
12
A
HIS
12
binding site for residue IOD A 301
A
IOD
301
Software
4
binding site for residue IOD A 303
A
IOD
303
Software
1
binding site for residue IOD A 304
A
IOD
304
Software
1
binding site for residue IOD A 306
A
IOD
306
Software
1
binding site for residue IOD A 307
A
IOD
307
Software
1
binding site for residue IOD A 308
A
IOD
308
Software
1
binding site for residue IOD A 309
A
IOD
309
Software
1
binding site for residue CL A 310
A
CL
310
Software
3
binding site for residue CL A 311
A
CL
311
Software
2
binding site for residue CL A 313
A
CL
313
Software
3
binding site for residue CL A 314
A
CL
314
Software
2
binding site for residue CL A 315
A
CL
315
Software
3
A
ALA
92
A
ALA
92
4
6_554
A
GLN
95
A
GLN
95
4
6_554
A
PRO
157
A
PRO
157
4
1_555
A
LYS
158
A
LYS
158
4
1_555
A
MET
144
A
MET
144
1
6_555
A
ASN
57
A
ASN
57
1
6_555
A
ARG
18
A
ARG
18
1
1_555
A
PRO
17
A
PRO
17
1
1_555
A
ASN
74
A
ASN
74
1
1_555
A
ASN
21
A
ASN
21
1
1_555
A
PHE
161
A
PHE
161
3
1_555
A
ARG
162
A
ARG
162
3
1_555
A
HOH
419
Q
HOH
3
1_555
A
ILE
129
A
ILE
129
2
1_555
A
HOH
441
Q
HOH
2
1_555
A
PRO
38
A
PRO
38
3
1_555
A
ARG
173
A
ARG
173
3
1_555
A
HOH
413
Q
HOH
3
1_555
A
GLY
60
A
GLY
60
2
1_555
A
HIS
62
A
HIS
62
2
1_555
A
ALA
31
A
ALA
31
3
1_555
A
PHE
32
A
PHE
32
3
1_555
A
TYR
145
A
TYR
145
3
1_555
168
P 6