0.020988
0.000000
0.004057
0.000000
0.013611
0.000000
0.000000
0.000000
0.009319
0.00000
0.00000
0.00000
Joyce, M.G.
Biertumpfel, C.
Nabel, G.J.
Kwong, P.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
100.94
90.00
47.647
73.471
109.292
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
Ca 2
40.078
CALCIUM 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
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
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
CA
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
N
N
160
S
C
N
161
N
C
N
162
N
O
N
163
S
C
N
164
N
C
N
165
N
C
N
166
N
C
N
167
N
O
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
N
N
182
S
C
N
183
N
C
N
184
N
O
N
185
N
C
N
186
N
C
N
187
N
C
N
188
N
C
N
189
N
O
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
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
N
N
204
S
C
N
205
N
C
N
206
N
O
N
207
N
C
N
208
N
C
N
209
N
C
N
210
N
C
N
211
N
N
N
212
N
O
N
213
N
H
N
214
N
H
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
N
N
229
S
C
N
230
N
C
N
231
N
O
N
232
N
C
N
233
N
C
N
234
N
S
N
235
N
C
N
236
N
O
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
N
N
249
S
C
N
250
N
C
N
251
N
O
N
252
N
C
Y
253
N
C
Y
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
N
259
N
O
N
260
N
H
N
261
N
H
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
N
N
272
S
C
N
273
N
C
N
274
N
O
N
275
N
C
N
276
N
C
N
277
N
C
N
278
N
O
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
H
N
288
N
N
N
289
S
C
N
290
N
C
N
291
N
O
N
292
N
C
N
293
N
O
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
N
N
303
S
C
N
304
N
C
N
305
N
O
N
306
R
C
N
307
N
O
N
308
N
C
N
309
N
O
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
N
N
320
S
C
N
321
N
C
N
322
N
O
N
323
N
C
Y
324
N
C
Y
325
N
C
Y
326
N
C
Y
327
N
N
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
Y
332
N
C
N
333
N
O
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
N
N
347
S
C
N
348
N
C
N
349
N
O
N
350
N
C
Y
351
N
C
Y
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
N
357
N
O
N
358
N
O
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
N
N
371
S
C
N
372
N
C
N
373
N
O
N
374
N
C
N
375
N
C
N
376
N
C
N
377
N
O
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
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
doub
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
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
doub
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
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
doub
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
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
doub
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
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
doub
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
Y
246
N
doub
Y
247
N
sing
Y
248
N
sing
N
249
N
sing
Y
250
N
doub
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
doub
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
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
doub
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
doub
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
doub
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
Y
315
N
doub
Y
316
N
sing
Y
317
N
sing
N
318
N
sing
Y
319
N
doub
Y
320
N
sing
Y
321
N
sing
N
322
N
sing
Y
323
N
sing
Y
324
N
doub
N
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
doub
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
Y
343
N
doub
Y
344
N
sing
Y
345
N
sing
N
346
N
sing
Y
347
N
doub
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
doub
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
US
J.Virol.
JOVIAM
0825
0022-538X
87
2294
2306
10.1128/JVI.02717-12
23236069
Outer Domain of HIV-1 gp120: Antigenic Optimization, Structural Malleability, and Crystal Structure with Antibody VRC-PG04.
2013
10.2210/pdb4i3s/pdb
pdb_00004i3s
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
2012-06-26
MARMOSAIC 300 mm CCD
Si 111 CHANNEL
SINGLE WAVELENGTH
M
x-ray
1
1
1.0
22-ID
APS
1
SYNCHROTRON
APS BEAMLINE 22-ID
20774.172
Outer domain of HIV-1 gp120 (KER2018 OD4.2.2)
1
man
polymer
24644.771
Heavy chain of VRC-PG04 Fab
1
man
polymer
23073.822
Light chain of VRC-PG04 Fab
1
man
polymer
40.078
CALCIUM ION
1
syn
non-polymer
no
no
KPVVSTQLLLNGSLAEKEIRIKSEDISDNAKNIIVQLTKPVLINCARPSNNTQYCVVNRTQWNDTLGQVAIQLRKHWNTC
IIFNEPSGGDLEITTHSFNCGGEFFYCNTSDLFNSTWNIEGTASIDGTESNDDITLPCRIKGSGAPPIQGVIRCQSNITG
ILLTRDGGSGSGTCETFRPGGGDMRDNWRS
KPVVSTQLLLNGSLAEKEIRIKSEDISDNAKNIIVQLTKPVLINCARPSNNTQYCVVNRTQWNDTLGQVAIQLRKHWNTC
IIFNEPSGGDLEITTHSFNCGGEFFYCNTSDLFNSTWNIEGTASIDGTESNDDITLPCRIKGSGAPPIQGVIRCQSNITG
ILLTRDGGSGSGTCETFRPGGGDMRDNWRS
G
polypeptide(L)
no
no
QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFT
AHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPE
PVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC
QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFT
AHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPE
PVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC
H
polypeptide(L)
no
no
EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPED
FARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQ
DSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPED
FARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQ
DSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
L
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
sample
12721
Human Immunodeficiency Virus
293S
9606
Homo sapiens
human
human
sample
9606
Homo sapiens
293F
9606
Homo sapiens
human
human
sample
9606
Homo sapiens
293F
9606
Homo sapiens
1
2.74
55.15
VAPOR DIFFUSION, HANGING DROP
7.5
52.5% peg 400, 100 mM HEPES pH7.5, 200 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
entity_src_gen
struct_conn
struct_conn_type
struct_site
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_conn_type
repository
Initial release
Database references
Database references
Derived calculations
Source and taxonomy
Data collection
Database references
Refinement description
Derived calculations
1
0
2013-01-09
1
1
2013-01-23
1
2
2013-02-13
1
3
2021-05-26
1
4
2023-09-20
1
5
2023-12-27
_entity_src_gen.gene_src_common_name
_entity_src_gen.host_org_common_name
_entity_src_gen.pdbx_host_org_cell_line
_entity_src_gen.pdbx_host_org_strain
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_seq_id
RCSB
Y
RCSB
2012-11-26
REL
REL
CA
CALCIUM ION
3SE9
PDB ENTRY 3SE9
PDB
experimental model
CA
1
4
CA
CA
301
L
LYS
252
n
1
LYS
252
G
PRO
253
n
2
PRO
253
G
VAL
254
n
3
VAL
254
G
VAL
255
n
4
VAL
255
G
SER
256
n
5
SER
256
G
THR
257
n
6
THR
257
G
GLN
258
n
7
GLN
258
G
LEU
259
n
8
LEU
259
G
LEU
260
n
9
LEU
260
G
LEU
261
n
10
LEU
261
G
ASN
262
n
11
ASN
262
G
GLY
263
n
12
GLY
263
G
SER
264
n
13
SER
264
G
LEU
265
n
14
LEU
265
G
ALA
266
n
15
ALA
266
G
GLU
267
n
16
GLU
267
G
LYS
268
n
17
LYS
268
G
GLU
269
n
18
GLU
269
G
ILE
270
n
19
ILE
270
G
ARG
271
n
20
ARG
271
G
ILE
272
n
21
ILE
272
G
LYS
273
n
22
LYS
273
G
SER
274
n
23
SER
274
G
GLU
275
n
24
GLU
275
G
ASP
276
n
25
ASP
276
G
ILE
277
n
26
ILE
277
G
SER
278
n
27
SER
278
G
ASP
279
n
28
ASP
279
G
ASN
280
n
29
ASN
280
G
ALA
281
n
30
ALA
281
G
LYS
282
n
31
LYS
282
G
ASN
283
n
32
ASN
283
G
ILE
284
n
33
ILE
284
G
ILE
285
n
34
ILE
285
G
VAL
286
n
35
VAL
286
G
GLN
287
n
36
GLN
287
G
LEU
288
n
37
LEU
288
G
THR
289
n
38
THR
289
G
LYS
290
n
39
LYS
290
G
PRO
291
n
40
PRO
291
G
VAL
292
n
41
VAL
292
G
LEU
293
n
42
LEU
293
G
ILE
294
n
43
ILE
294
G
ASN
295
n
44
ASN
295
G
CYS
296
n
45
CYS
296
G
ALA
297
n
46
ALA
297
G
ARG
298
n
47
ARG
298
G
PRO
299
n
48
PRO
299
G
SER
300
n
49
SER
300
G
ASN
301
n
50
ASN
301
G
ASN
302
n
51
ASN
302
G
THR
303
n
52
THR
303
G
GLN
304
n
53
GLN
304
G
TYR
330
n
54
TYR
330
G
CYS
331
n
55
CYS
331
G
VAL
332
n
56
VAL
332
G
VAL
333
n
57
VAL
333
G
ASN
334
n
58
ASN
334
G
ARG
335
n
59
ARG
335
G
THR
336
n
60
THR
336
G
GLN
337
n
61
GLN
337
G
TRP
338
n
62
TRP
338
G
ASN
339
n
63
ASN
339
G
ASP
340
n
64
ASP
340
G
THR
341
n
65
THR
341
G
LEU
342
n
66
LEU
342
G
GLY
343
n
67
GLY
343
G
GLN
344
n
68
GLN
344
G
VAL
345
n
69
VAL
345
G
ALA
346
n
70
ALA
346
G
ILE
347
n
71
ILE
347
G
GLN
348
n
72
GLN
348
G
LEU
349
n
73
LEU
349
G
ARG
350
n
74
ARG
350
G
LYS
351
n
75
LYS
351
G
HIS
352
n
76
HIS
352
G
TRP
353
n
77
TRP
353
G
ASN
356
n
78
ASN
356
G
THR
357
n
79
THR
357
G
CYS
358
n
80
CYS
358
G
ILE
359
n
81
ILE
359
G
ILE
360
n
82
ILE
360
G
PHE
361
n
83
PHE
361
G
ASN
362
n
84
ASN
362
G
GLU
363
n
85
GLU
363
G
PRO
364
n
86
PRO
364
G
SER
365
n
87
SER
365
G
GLY
366
n
88
GLY
366
G
GLY
367
n
89
GLY
367
G
ASP
368
n
90
ASP
368
G
LEU
369
n
91
LEU
369
G
GLU
370
n
92
GLU
370
G
ILE
371
n
93
ILE
371
G
THR
372
n
94
THR
372
G
THR
373
n
95
THR
373
G
HIS
374
n
96
HIS
374
G
SER
375
n
97
SER
375
G
PHE
376
n
98
PHE
376
G
ASN
377
n
99
ASN
377
G
CYS
378
n
100
CYS
378
G
GLY
379
n
101
GLY
379
G
GLY
380
n
102
GLY
380
G
GLU
381
n
103
GLU
381
G
PHE
382
n
104
PHE
382
G
PHE
383
n
105
PHE
383
G
TYR
384
n
106
TYR
384
G
CYS
385
n
107
CYS
385
G
ASN
386
n
108
ASN
386
G
THR
387
n
109
THR
387
G
SER
388
n
110
SER
388
G
ASP
389
n
111
ASP
389
G
LEU
390
n
112
LEU
390
G
PHE
391
n
113
PHE
391
G
ASN
392
n
114
ASN
392
G
SER
393
n
115
SER
393
G
THR
394
n
116
THR
394
G
TRP
395
n
117
TRP
395
G
ASN
395
n
118
A
ASN
395
G
ILE
396
n
119
ILE
396
G
GLU
397
n
120
GLU
397
G
GLY
398
n
121
GLY
398
G
THR
399
n
122
THR
399
G
ALA
400
n
123
ALA
400
G
SER
401
n
124
SER
401
G
ILE
402
n
125
ILE
402
G
ASP
403
n
126
ASP
403
G
n
127
407
G
n
128
408
G
n
129
409
G
n
130
410
G
n
131
411
G
n
132
412
G
ASP
413
n
133
ASP
413
G
ILE
414
n
134
ILE
414
G
THR
415
n
135
THR
415
G
LEU
416
n
136
LEU
416
G
PRO
417
n
137
PRO
417
G
CYS
418
n
138
CYS
418
G
ARG
419
n
139
ARG
419
G
ILE
420
n
140
ILE
420
G
LYS
421
n
141
LYS
421
G
GLY
431
n
142
GLY
431
G
SER
432
n
143
SER
432
G
GLY
433
n
144
GLY
433
G
ALA
436
n
145
ALA
436
G
PRO
437
n
146
PRO
437
G
PRO
438
n
147
PRO
438
G
ILE
439
n
148
ILE
439
G
GLN
440
n
149
GLN
440
G
GLY
441
n
150
GLY
441
G
VAL
442
n
151
VAL
442
G
ILE
443
n
152
ILE
443
G
ARG
444
n
153
ARG
444
G
CYS
445
n
154
CYS
445
G
GLN
446
n
155
GLN
446
G
SER
447
n
156
SER
447
G
ASN
448
n
157
ASN
448
G
ILE
449
n
158
ILE
449
G
THR
450
n
159
THR
450
G
GLY
451
n
160
GLY
451
G
ILE
452
n
161
ILE
452
G
LEU
453
n
162
LEU
453
G
LEU
454
n
163
LEU
454
G
THR
455
n
164
THR
455
G
ARG
456
n
165
ARG
456
G
ASP
457
n
166
ASP
457
G
GLY
458
n
167
GLY
458
G
GLY
459
n
168
GLY
459
G
SER
460
n
169
SER
460
G
GLY
461
n
170
GLY
461
G
SER
462
n
171
SER
462
G
GLY
463
n
172
GLY
463
G
THR
464
n
173
THR
464
G
CYS
465
n
174
CYS
465
G
GLU
466
n
175
GLU
466
G
THR
467
n
176
THR
467
G
PHE
468
n
177
PHE
468
G
ARG
469
n
178
ARG
469
G
PRO
470
n
179
PRO
470
G
GLY
471
n
180
GLY
471
G
GLY
472
n
181
GLY
472
G
GLY
473
n
182
GLY
473
G
ASP
474
n
183
ASP
474
G
MET
475
n
184
MET
475
G
ARG
476
n
185
ARG
476
G
ASP
477
n
186
ASP
477
G
n
187
478
G
n
188
479
G
n
189
480
G
n
190
481
G
GLN
1
n
1
GLN
1
H
VAL
2
n
2
VAL
2
H
GLN
3
n
3
GLN
3
H
LEU
4
n
4
LEU
4
H
VAL
5
n
5
VAL
5
H
GLN
6
n
6
GLN
6
H
SER
7
n
7
SER
7
H
GLY
8
n
8
GLY
8
H
SER
9
n
9
SER
9
H
GLY
10
n
10
GLY
10
H
VAL
11
n
11
VAL
11
H
LYS
12
n
12
LYS
12
H
LYS
13
n
13
LYS
13
H
PRO
14
n
14
PRO
14
H
GLY
15
n
15
GLY
15
H
ALA
16
n
16
ALA
16
H
SER
17
n
17
SER
17
H
VAL
18
n
18
VAL
18
H
ARG
19
n
19
ARG
19
H
VAL
20
n
20
VAL
20
H
SER
21
n
21
SER
21
H
CYS
22
n
22
CYS
22
H
TRP
23
n
23
TRP
23
H
THR
24
n
24
THR
24
H
SER
25
n
25
SER
25
H
GLU
26
n
26
GLU
26
H
ASP
27
n
27
ASP
27
H
ILE
28
n
28
ILE
28
H
PHE
29
n
29
PHE
29
H
GLU
30
n
30
GLU
30
H
ARG
31
n
31
ARG
31
H
THR
32
n
32
THR
32
H
GLU
33
n
33
GLU
33
H
LEU
34
n
34
LEU
34
H
ILE
35
n
35
ILE
35
H
HIS
35
n
36
A
HIS
35
H
TRP
36
n
37
TRP
36
H
VAL
37
n
38
VAL
37
H
ARG
38
n
39
ARG
38
H
GLN
39
n
40
GLN
39
H
ALA
40
n
41
ALA
40
H
PRO
41
n
42
PRO
41
H
GLY
42
n
43
GLY
42
H
GLN
43
n
44
GLN
43
H
GLY
44
n
45
GLY
44
H
LEU
45
n
46
LEU
45
H
GLU
46
n
47
GLU
46
H
TRP
47
n
48
TRP
47
H
ILE
48
n
49
ILE
48
H
GLY
49
n
50
GLY
49
H
TRP
50
n
51
TRP
50
H
VAL
51
n
52
VAL
51
H
LYS
52
n
53
LYS
52
H
THR
52
n
54
A
THR
52
H
VAL
52
n
55
B
VAL
52
H
THR
53
n
56
THR
53
H
GLY
54
n
57
GLY
54
H
ALA
55
n
58
ALA
55
H
VAL
56
n
59
VAL
56
H
ASN
57
n
60
ASN
57
H
PHE
58
n
61
PHE
58
H
GLY
59
n
62
GLY
59
H
SER
60
n
63
SER
60
H
PRO
61
n
64
PRO
61
H
ASP
62
n
65
ASP
62
H
PHE
63
n
66
PHE
63
H
ARG
64
n
67
ARG
64
H
GLN
65
n
68
GLN
65
H
ARG
66
n
69
ARG
66
H
VAL
67
n
70
VAL
67
H
SER
68
n
71
SER
68
H
LEU
69
n
72
LEU
69
H
THR
70
n
73
THR
70
H
ARG
71
n
74
ARG
71
H
ASP
72
n
75
ASP
72
H
ARG
73
n
76
ARG
73
H
ASP
74
n
77
ASP
74
H
LEU
75
n
78
LEU
75
H
PHE
76
n
79
PHE
76
H
THR
77
n
80
THR
77
H
ALA
78
n
81
ALA
78
H
HIS
79
n
82
HIS
79
H
MET
80
n
83
MET
80
H
ASP
81
n
84
ASP
81
H
ILE
82
n
85
ILE
82
H
ARG
82
n
86
A
ARG
82
H
GLY
82
n
87
B
GLY
82
H
LEU
82
n
88
C
LEU
82
H
THR
83
n
89
THR
83
H
GLN
84
n
90
GLN
84
H
GLY
85
n
91
GLY
85
H
ASP
86
n
92
ASP
86
H
THR
87
n
93
THR
87
H
ALA
88
n
94
ALA
88
H
THR
89
n
95
THR
89
H
TYR
90
n
96
TYR
90
H
PHE
91
n
97
PHE
91
H
CYS
92
n
98
CYS
92
H
ALA
93
n
99
ALA
93
H
ARG
94
n
100
ARG
94
H
GLN
95
n
101
GLN
95
H
LYS
96
n
102
LYS
96
H
PHE
97
n
103
PHE
97
H
TYR
98
n
104
TYR
98
H
THR
99
n
105
THR
99
H
GLY
100
n
106
GLY
100
H
GLY
100
n
107
A
GLY
100
H
GLN
100
n
108
B
GLN
100
H
GLY
100
n
109
C
GLY
100
H
TRP
100
n
110
D
TRP
100
H
TYR
100
n
111
E
TYR
100
H
PHE
100
n
112
F
PHE
100
H
ASP
101
n
113
ASP
101
H
LEU
102
n
114
LEU
102
H
TRP
103
n
115
TRP
103
H
GLY
104
n
116
GLY
104
H
ARG
105
n
117
ARG
105
H
GLY
106
n
118
GLY
106
H
THR
107
n
119
THR
107
H
LEU
108
n
120
LEU
108
H
ILE
109
n
121
ILE
109
H
VAL
110
n
122
VAL
110
H
VAL
111
n
123
VAL
111
H
SER
112
n
124
SER
112
H
SER
113
n
125
SER
113
H
ALA
114
n
126
ALA
114
H
SER
115
n
127
SER
115
H
THR
116
n
128
THR
116
H
LYS
117
n
129
LYS
117
H
GLY
118
n
130
GLY
118
H
PRO
119
n
131
PRO
119
H
SER
120
n
132
SER
120
H
VAL
121
n
133
VAL
121
H
PHE
122
n
134
PHE
122
H
PRO
123
n
135
PRO
123
H
LEU
124
n
136
LEU
124
H
ALA
125
n
137
ALA
125
H
PRO
126
n
138
PRO
126
H
SER
127
n
139
SER
127
H
n
140
128
H
n
141
129
H
n
142
130
H
n
143
131
H
n
144
132
H
GLY
133
n
145
GLY
133
H
GLY
134
n
146
GLY
134
H
THR
135
n
147
THR
135
H
ALA
136
n
148
ALA
136
H
ALA
137
n
149
ALA
137
H
LEU
138
n
150
LEU
138
H
GLY
139
n
151
GLY
139
H
CYS
140
n
152
CYS
140
H
LEU
141
n
153
LEU
141
H
VAL
142
n
154
VAL
142
H
LYS
143
n
155
LYS
143
H
ASP
144
n
156
ASP
144
H
TYR
145
n
157
TYR
145
H
PHE
146
n
158
PHE
146
H
PRO
147
n
159
PRO
147
H
GLU
148
n
160
GLU
148
H
PRO
149
n
161
PRO
149
H
VAL
150
n
162
VAL
150
H
THR
151
n
163
THR
151
H
VAL
152
n
164
VAL
152
H
SER
153
n
165
SER
153
H
TRP
154
n
166
TRP
154
H
ASN
155
n
167
ASN
155
H
SER
156
n
168
SER
156
H
GLY
157
n
169
GLY
157
H
ALA
158
n
170
ALA
158
H
LEU
159
n
171
LEU
159
H
THR
160
n
172
THR
160
H
SER
161
n
173
SER
161
H
GLY
162
n
174
GLY
162
H
VAL
163
n
175
VAL
163
H
HIS
164
n
176
HIS
164
H
THR
165
n
177
THR
165
H
PHE
166
n
178
PHE
166
H
PRO
167
n
179
PRO
167
H
ALA
168
n
180
ALA
168
H
VAL
169
n
181
VAL
169
H
LEU
170
n
182
LEU
170
H
GLN
171
n
183
GLN
171
H
SER
172
n
184
SER
172
H
SER
173
n
185
SER
173
H
GLY
174
n
186
GLY
174
H
LEU
175
n
187
LEU
175
H
TYR
176
n
188
TYR
176
H
SER
177
n
189
SER
177
H
LEU
178
n
190
LEU
178
H
SER
179
n
191
SER
179
H
SER
180
n
192
SER
180
H
VAL
181
n
193
VAL
181
H
VAL
182
n
194
VAL
182
H
THR
183
n
195
THR
183
H
VAL
184
n
196
VAL
184
H
PRO
185
n
197
PRO
185
H
SER
186
n
198
SER
186
H
SER
187
n
199
SER
187
H
SER
188
n
200
SER
188
H
LEU
189
n
201
LEU
189
H
GLY
190
n
202
GLY
190
H
THR
191
n
203
THR
191
H
GLN
192
n
204
GLN
192
H
THR
193
n
205
THR
193
H
TYR
194
n
206
TYR
194
H
ILE
195
n
207
ILE
195
H
CYS
196
n
208
CYS
196
H
ASN
197
n
209
ASN
197
H
VAL
198
n
210
VAL
198
H
ASN
199
n
211
ASN
199
H
HIS
200
n
212
HIS
200
H
LYS
201
n
213
LYS
201
H
PRO
202
n
214
PRO
202
H
SER
203
n
215
SER
203
H
ASN
204
n
216
ASN
204
H
THR
205
n
217
THR
205
H
LYS
206
n
218
LYS
206
H
VAL
207
n
219
VAL
207
H
ASP
208
n
220
ASP
208
H
LYS
209
n
221
LYS
209
H
LYS
210
n
222
LYS
210
H
VAL
211
n
223
VAL
211
H
GLU
212
n
224
GLU
212
H
PRO
213
n
225
PRO
213
H
LYS
214
n
226
LYS
214
H
SER
215
n
227
SER
215
H
n
228
216
H
GLU
1
n
1
GLU
1
L
ILE
2
n
2
ILE
2
L
VAL
3
n
3
VAL
3
L
LEU
4
n
4
LEU
4
L
THR
5
n
5
THR
5
L
GLN
6
n
6
GLN
6
L
SER
7
n
7
SER
7
L
PRO
8
n
8
PRO
8
L
GLY
9
n
9
GLY
9
L
THR
10
n
10
THR
10
L
LEU
11
n
11
LEU
11
L
SER
12
n
12
SER
12
L
LEU
13
n
13
LEU
13
L
SER
14
n
14
SER
14
L
PRO
15
n
15
PRO
15
L
GLY
16
n
16
GLY
16
L
GLU
17
n
17
GLU
17
L
THR
18
n
18
THR
18
L
ALA
19
n
19
ALA
19
L
SER
20
n
20
SER
20
L
LEU
21
n
21
LEU
21
L
SER
22
n
22
SER
22
L
CYS
23
n
23
CYS
23
L
THR
24
n
24
THR
24
L
ALA
25
n
25
ALA
25
L
ALA
26
n
26
ALA
26
L
SER
27
n
27
SER
27
L
TYR
30
n
28
TYR
30
L
GLY
31
n
29
GLY
31
L
HIS
32
n
30
HIS
32
L
MET
33
n
31
MET
33
L
THR
34
n
32
THR
34
L
TRP
35
n
33
TRP
35
L
TYR
36
n
34
TYR
36
L
GLN
37
n
35
GLN
37
L
LYS
38
n
36
LYS
38
L
LYS
39
n
37
LYS
39
L
PRO
40
n
38
PRO
40
L
GLY
41
n
39
GLY
41
L
GLN
42
n
40
GLN
42
L
PRO
43
n
41
PRO
43
L
PRO
44
n
42
PRO
44
L
LYS
45
n
43
LYS
45
L
LEU
46
n
44
LEU
46
L
LEU
47
n
45
LEU
47
L
ILE
48
n
46
ILE
48
L
PHE
49
n
47
PHE
49
L
ALA
50
n
48
ALA
50
L
THR
51
n
49
THR
51
L
SER
52
n
50
SER
52
L
LYS
53
n
51
LYS
53
L
ARG
54
n
52
ARG
54
L
ALA
55
n
53
ALA
55
L
SER
56
n
54
SER
56
L
GLY
57
n
55
GLY
57
L
ILE
58
n
56
ILE
58
L
PRO
59
n
57
PRO
59
L
ASP
60
n
58
ASP
60
L
ARG
61
n
59
ARG
61
L
PHE
62
n
60
PHE
62
L
SER
63
n
61
SER
63
L
GLY
64
n
62
GLY
64
L
SER
65
n
63
SER
65
L
GLN
66
n
64
GLN
66
L
PHE
67
n
65
PHE
67
L
GLY
68
n
66
GLY
68
L
LYS
69
n
67
LYS
69
L
GLN
70
n
68
GLN
70
L
TYR
71
n
69
TYR
71
L
THR
72
n
70
THR
72
L
LEU
73
n
71
LEU
73
L
THR
74
n
72
THR
74
L
ILE
75
n
73
ILE
75
L
THR
76
n
74
THR
76
L
ARG
77
n
75
ARG
77
L
MET
78
n
76
MET
78
L
GLU
79
n
77
GLU
79
L
PRO
80
n
78
PRO
80
L
GLU
81
n
79
GLU
81
L
ASP
82
n
80
ASP
82
L
PHE
83
n
81
PHE
83
L
ALA
84
n
82
ALA
84
L
ARG
85
n
83
ARG
85
L
TYR
86
n
84
TYR
86
L
TYR
87
n
85
TYR
87
L
CYS
88
n
86
CYS
88
L
GLN
89
n
87
GLN
89
L
GLN
90
n
88
GLN
90
L
LEU
91
n
89
LEU
91
L
GLU
96
n
90
GLU
96
L
PHE
97
n
91
PHE
97
L
PHE
98
n
92
PHE
98
L
GLY
99
n
93
GLY
99
L
GLN
100
n
94
GLN
100
L
GLY
101
n
95
GLY
101
L
THR
102
n
96
THR
102
L
ARG
103
n
97
ARG
103
L
LEU
104
n
98
LEU
104
L
GLU
105
n
99
GLU
105
L
ILE
106
n
100
ILE
106
L
ARG
107
n
101
ARG
107
L
ARG
108
n
102
ARG
108
L
THR
109
n
103
THR
109
L
VAL
110
n
104
VAL
110
L
ALA
111
n
105
ALA
111
L
ALA
112
n
106
ALA
112
L
PRO
113
n
107
PRO
113
L
SER
114
n
108
SER
114
L
VAL
115
n
109
VAL
115
L
PHE
116
n
110
PHE
116
L
ILE
117
n
111
ILE
117
L
PHE
118
n
112
PHE
118
L
PRO
119
n
113
PRO
119
L
PRO
120
n
114
PRO
120
L
SER
121
n
115
SER
121
L
ASP
122
n
116
ASP
122
L
GLU
123
n
117
GLU
123
L
GLN
124
n
118
GLN
124
L
LEU
125
n
119
LEU
125
L
LYS
126
n
120
LYS
126
L
SER
127
n
121
SER
127
L
GLY
128
n
122
GLY
128
L
THR
129
n
123
THR
129
L
ALA
130
n
124
ALA
130
L
SER
131
n
125
SER
131
L
VAL
132
n
126
VAL
132
L
VAL
133
n
127
VAL
133
L
CYS
134
n
128
CYS
134
L
LEU
135
n
129
LEU
135
L
LEU
136
n
130
LEU
136
L
ASN
137
n
131
ASN
137
L
ASN
138
n
132
ASN
138
L
PHE
139
n
133
PHE
139
L
TYR
140
n
134
TYR
140
L
PRO
141
n
135
PRO
141
L
ARG
142
n
136
ARG
142
L
GLU
143
n
137
GLU
143
L
ALA
144
n
138
ALA
144
L
LYS
145
n
139
LYS
145
L
VAL
146
n
140
VAL
146
L
GLN
147
n
141
GLN
147
L
TRP
148
n
142
TRP
148
L
LYS
149
n
143
LYS
149
L
VAL
150
n
144
VAL
150
L
ASP
151
n
145
ASP
151
L
ASN
152
n
146
ASN
152
L
ALA
153
n
147
ALA
153
L
LEU
154
n
148
LEU
154
L
GLN
155
n
149
GLN
155
L
SER
156
n
150
SER
156
L
GLY
157
n
151
GLY
157
L
ASN
158
n
152
ASN
158
L
SER
159
n
153
SER
159
L
GLN
160
n
154
GLN
160
L
GLU
161
n
155
GLU
161
L
SER
162
n
156
SER
162
L
VAL
163
n
157
VAL
163
L
THR
164
n
158
THR
164
L
GLU
165
n
159
GLU
165
L
GLN
166
n
160
GLN
166
L
ASP
167
n
161
ASP
167
L
SER
168
n
162
SER
168
L
LYS
169
n
163
LYS
169
L
ASP
170
n
164
ASP
170
L
SER
171
n
165
SER
171
L
THR
172
n
166
THR
172
L
TYR
173
n
167
TYR
173
L
SER
174
n
168
SER
174
L
LEU
175
n
169
LEU
175
L
SER
176
n
170
SER
176
L
SER
177
n
171
SER
177
L
THR
178
n
172
THR
178
L
LEU
179
n
173
LEU
179
L
THR
180
n
174
THR
180
L
LEU
181
n
175
LEU
181
L
SER
182
n
176
SER
182
L
LYS
183
n
177
LYS
183
L
ALA
184
n
178
ALA
184
L
ASP
185
n
179
ASP
185
L
TYR
186
n
180
TYR
186
L
GLU
187
n
181
GLU
187
L
LYS
188
n
182
LYS
188
L
HIS
189
n
183
HIS
189
L
LYS
190
n
184
LYS
190
L
VAL
191
n
185
VAL
191
L
TYR
192
n
186
TYR
192
L
ALA
193
n
187
ALA
193
L
CYS
194
n
188
CYS
194
L
GLU
195
n
189
GLU
195
L
VAL
196
n
190
VAL
196
L
THR
197
n
191
THR
197
L
HIS
198
n
192
HIS
198
L
GLN
199
n
193
GLN
199
L
GLY
200
n
194
GLY
200
L
LEU
201
n
195
LEU
201
L
SER
202
n
196
SER
202
L
SER
203
n
197
SER
203
L
PRO
204
n
198
PRO
204
L
VAL
205
n
199
VAL
205
L
THR
206
n
200
THR
206
L
LYS
207
n
201
LYS
207
L
SER
208
n
202
SER
208
L
PHE
209
n
203
PHE
209
L
ASN
210
n
204
ASN
210
L
ARG
211
n
205
ARG
211
L
GLY
212
n
206
GLY
212
L
GLU
213
n
207
GLU
213
L
CYS
214
n
208
CYS
214
L
1.6014
-0.6235
-1.0290
0.9787
0.3716
0.9498
-0.0231
0.1198
-0.1797
-0.0352
-0.0144
0.1216
-0.0373
0.0454
0.0375
-0.1664
-0.0586
0.1713
-0.3713
-0.0357
0.0587
refined
7.0622
-16.8376
23.6352
X-RAY DIFFRACTION
G
252
G
477
X-RAY DIFFRACTION
1
{ *|* }
H
1
H
215
X-RAY DIFFRACTION
1
{ *|* }
L
1
L
214
X-RAY DIFFRACTION
1
{ *|* }
L
301
L
301
X-RAY DIFFRACTION
1
{ *|* }
author_defined_assembly
3
trimeric
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
G
N
LEU
260
A
N
LEU
9
G
O
GLY
451
A
O
GLY
160
G
O
ILE
449
A
O
ILE
158
G
N
VAL
292
A
N
VAL
41
G
N
ASN
295
A
N
ASN
44
G
O
VAL
332
A
O
VAL
56
G
N
CYS
331
A
N
CYS
55
G
O
LEU
416
A
O
LEU
136
G
O
ARG
419
A
O
ARG
139
G
N
TYR
384
A
N
TYR
106
G
O
PHE
383
A
O
PHE
105
G
N
PHE
376
A
N
PHE
98
G
N
LYS
273
A
N
LYS
22
G
O
ILE
285
A
O
ILE
34
G
N
VAL
292
A
N
VAL
41
G
O
ILE
449
A
O
ILE
158
G
N
THR
455
A
N
THR
164
G
O
ARG
469
A
O
ARG
178
G
O
GLU
466
A
O
GLU
175
G
N
ILE
360
A
N
ILE
82
G
N
ILE
359
A
N
ILE
81
G
O
TRP
395
A
O
TRP
117
H
N
VAL
5
B
N
VAL
5
H
O
TRP
23
B
O
TRP
23
H
N
VAL
20
B
N
VAL
20
H
O
MET
80
B
O
MET
83
H
O
HIS
79
B
O
HIS
82
H
N
THR
70
B
N
THR
73
H
N
LYS
12
B
N
LYS
12
H
O
VAL
110
B
O
VAL
122
H
O
THR
107
B
O
THR
119
H
N
TYR
90
B
N
TYR
96
H
O
THR
89
B
O
THR
95
H
N
GLN
39
B
N
GLN
40
H
N
ARG
38
B
N
ARG
39
H
O
GLU
46
B
O
GLU
47
H
N
TRP
50
B
N
TRP
51
H
O
ASN
57
B
O
ASN
60
H
N
LYS
12
B
N
LYS
12
H
O
VAL
110
B
O
VAL
122
H
O
THR
107
B
O
THR
119
H
N
TYR
90
B
N
TYR
96
H
N
ARG
94
B
N
ARG
100
H
O
LEU
102
B
O
LEU
114
H
N
LEU
124
B
N
LEU
136
H
O
GLY
139
B
O
GLY
151
H
N
LEU
138
B
N
LEU
150
H
O
VAL
182
B
O
VAL
194
H
O
VAL
181
B
O
VAL
193
H
N
HIS
164
B
N
HIS
176
H
N
LEU
124
B
N
LEU
136
H
O
GLY
139
B
O
GLY
151
H
N
LEU
138
B
N
LEU
150
H
O
VAL
182
B
O
VAL
194
H
O
SER
177
B
O
SER
189
H
N
VAL
169
B
N
VAL
181
H
N
THR
151
B
N
THR
163
H
O
ASN
199
B
O
ASN
211
H
N
CYS
196
B
N
CYS
208
H
O
LYS
209
B
O
LYS
221
L
N
THR
5
C
N
THR
5
L
O
THR
24
C
O
THR
24
L
N
LEU
21
C
N
LEU
21
L
O
LEU
73
C
O
LEU
71
L
O
GLN
70
C
O
GLN
68
L
N
PHE
67
C
N
PHE
65
L
N
LEU
11
C
N
LEU
11
L
O
ARG
103
C
O
ARG
97
L
O
THR
102
C
O
THR
96
L
N
TYR
86
C
N
TYR
84
L
O
ARG
85
C
O
ARG
83
L
N
LYS
38
C
N
LYS
36
L
N
GLN
37
C
N
GLN
35
L
O
LYS
45
C
O
LYS
43
L
N
PHE
49
C
N
PHE
47
L
O
LYS
53
C
O
LYS
51
L
N
LEU
11
C
N
LEU
11
L
O
ARG
103
C
O
ARG
97
L
O
THR
102
C
O
THR
96
L
N
TYR
86
C
N
TYR
84
L
N
GLN
90
C
N
GLN
88
L
O
PHE
97
C
O
PHE
91
L
N
SER
114
C
N
SER
108
L
O
ASN
137
C
O
ASN
131
L
N
ALA
130
C
N
ALA
124
L
O
LEU
181
C
O
LEU
175
L
O
SER
176
C
O
SER
170
L
N
SER
162
C
N
SER
156
L
O
GLN
155
C
O
GLN
149
L
N
TRP
148
C
N
TRP
142
L
N
LYS
149
C
N
LYS
143
L
O
ALA
193
C
O
ALA
187
L
N
VAL
196
C
N
VAL
190
L
O
VAL
205
C
O
VAL
199
1
G
GLY
407
A
GLY
127
1
Y
1
G
THR
408
A
THR
128
1
Y
1
G
GLU
409
A
GLU
129
1
Y
1
G
SER
410
A
SER
130
1
Y
1
G
ASN
411
A
ASN
131
1
Y
1
G
ASP
412
A
ASP
132
1
Y
1
G
ASN
478
A
ASN
187
1
Y
1
G
TRP
479
A
TRP
188
1
Y
1
G
ARG
480
A
ARG
189
1
Y
1
G
SER
481
A
SER
190
1
Y
1
H
SER
128
B
SER
140
1
Y
1
H
LYS
129
B
LYS
141
1
Y
1
H
SER
130
B
SER
142
1
Y
1
H
THR
131
B
THR
143
1
Y
1
H
SER
132
B
SER
144
1
Y
1
H
CYS
216
B
CYS
228
1
Y
1
G
PRO
253
-85.77
-156.21
1
G
LYS
268
-121.10
-60.12
1
G
ASP
276
-165.69
107.22
1
G
ASN
302
-118.79
51.15
1
G
ASN
392
-176.03
46.83
1
G
GLU
397
-75.79
-164.17
1
G
PRO
437
-33.68
130.61
1
G
VAL
442
-114.94
65.91
1
G
THR
464
56.49
-116.62
1
H
VAL
2
-160.52
-158.47
B
1
H
VAL
52
-96.30
-76.36
1
H
PHE
97
-56.81
107.02
1
H
THR
116
-57.55
108.24
1
H
PRO
147
-93.43
-158.04
1
L
LEU
4
92.97
11.17
1
L
SER
7
-170.31
148.20
1
L
ALA
26
-63.64
1.28
1
L
THR
51
74.12
-56.55
1
L
LEU
91
61.69
-123.28
1
L
ASN
158
-151.02
-9.46
41.38
6.9102
0.0000
1.8997
-6.0238
0.0000
-0.8864
0.8262
0.7166
0.3199
0.2483
0.2534
2.85
46.78
1075
17504
14941
7.19
85.41
RANDOM
1
THROUGHOUT
0.0
0
MOLECULAR REPLACEMENT
PDB ENTRY 3SE9
MLHL
0.508
2.85
46.78
0
4690
1
0
4689
0.009
4801
HARMONIC
2.00
1.19
6518
HARMONIC
2.00
1629
SINUSOIDAL
2.00
111
HARMONIC
2.00
700
HARMONIC
5.00
4801
HARMONIC
20.00
2.43
22.68
639
SEMIHARMONIC
5.00
4978
SEMIHARMONIC
4.00
0.3110
0.2345
0.2405
3.05
180
2224
2404
8
7.49
85.41
47.83
2.85
50.0
4I3S
14947
2
2
0.225
0.225
1
6.21
2
85.4
0.90
2.85
2.93
2.01
0.90
1
1.3
76.3
data scaling
XDS
phasing
PHASER
refinement
BUSTER
2.10.0
data reduction
XDS
Crystal structure of the outer domain of HIV-1 gp120 in complex with VRC-PG04 space group P21
1
N
N
2
N
N
3
N
N
4
N
N
The Biological unit is identical to that found in the asymmetric unit.
The Biological unit is identical to that found in the asymmetric unit.
The Biological unit is identical to that found in the asymmetric unit.
G
ASN
334
A
ASN
58
HELX_P
G
ARG
350
A
ARG
74
1
1
17
G
ASP
368
A
ASP
90
HELX_P
G
THR
373
A
THR
95
1
2
6
H
SER
25
B
SER
25
HELX_P
H
GLU
30
B
GLU
30
1
3
6
H
SER
60
B
SER
63
HELX_P
H
GLN
65
B
GLN
68
1
4
6
H
THR
83
B
THR
89
HELX_P
H
THR
87
B
THR
93
5
5
5
H
SER
156
B
SER
168
HELX_P
H
ALA
158
B
ALA
170
5
6
3
L
GLU
79
C
GLU
77
HELX_P
L
PHE
83
C
PHE
81
5
7
5
L
SER
121
C
SER
115
HELX_P
L
LYS
126
C
LYS
120
1
8
6
L
LYS
183
C
LYS
177
HELX_P
L
LYS
188
C
LYS
182
1
9
6
disulf
2.900
G
CYS
296
A
SG
CYS
45
1_555
G
CYS
331
A
SG
CYS
55
1_555
disulf
2.463
G
CYS
358
A
SG
CYS
80
1_555
G
CYS
465
A
SG
CYS
174
1_555
disulf
2.502
G
CYS
378
A
SG
CYS
100
1_555
G
CYS
445
A
SG
CYS
154
1_555
disulf
1.537
none
G
CYS
385
A
SG
CYS
107
1_555
G
CYS
418
A
SG
CYS
138
1_555
disulf
2.816
H
CYS
22
B
SG
CYS
22
1_555
H
CYS
92
B
SG
CYS
98
1_555
disulf
2.998
H
CYS
140
B
SG
CYS
152
1_555
H
CYS
196
B
SG
CYS
208
1_555
disulf
2.541
L
CYS
134
C
SG
CYS
128
1_555
L
CYS
194
C
SG
CYS
188
1_555
metalc
2.642
L
GLU
143
C
OE1
GLU
137
1_555
L
CA
301
D
CA
CA
1_555
Viral Protein/Immune System
Antibody Affinity, Antibody Specificity, Binding Sites, HIV Infections, Antibodies, HIV Envelope Protein gp120, AIDS Vaccines, Amino Acid Sequence, Antigens, Epitopes, HIV Antibodies, CD4, Somatic Mutation, Sequence engineering, Complementarity Determining Regions, Immunoglobulin Fab Fragments, Sera, Viral Protein-Immune System complex
G
ASN
301
A
ASN
50
1
G
ASN
302
A
ASN
51
0.55
G
GLY
433
A
GLY
144
1
G
ALA
436
A
ALA
145
2.68
G
GLY
441
A
GLY
150
1
G
VAL
442
A
VAL
151
1.23
G
GLY
472
A
GLY
181
1
G
GLY
473
A
GLY
182
0.35
H
GLN
1
B
GLN
1
1
H
VAL
2
B
VAL
2
-1.74
H
GLN
3
B
GLN
3
1
H
LEU
4
B
LEU
4
-1.62
H
PHE
146
B
PHE
158
1
H
PRO
147
B
PRO
159
-5.75
H
GLU
148
B
GLU
160
1
H
PRO
149
B
PRO
161
6.41
L
SER
7
C
SER
7
1
L
PRO
8
C
PRO
8
-2.57
L
TYR
140
C
TYR
134
1
L
PRO
141
C
PRO
135
-5.05
4I3S
PDB
1
4I3S
4I3S
PDB
2
4I3S
4I3S
PDB
3
4I3S
252
481
4I3S
252
481
4I3S
G
1
1
190
1
216
4I3S
1
216
4I3S
H
2
1
228
1
214
4I3S
1
214
4I3S
L
3
1
208
7
6
4
6
4
4
4
3
4
6
4
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
G
LEU
259
A
LEU
8
G
LEU
261
A
LEU
10
G
ILE
443
A
ILE
152
G
ARG
456
A
ARG
165
G
ILE
284
A
ILE
33
G
ARG
298
A
ARG
47
G
TYR
330
A
TYR
54
G
VAL
333
A
VAL
57
G
ILE
414
A
ILE
134
G
ILE
420
A
ILE
140
G
GLU
381
A
GLU
103
G
CYS
385
A
CYS
107
G
HIS
374
A
HIS
96
G
CYS
378
A
CYS
100
G
ARG
271
A
ARG
20
G
LYS
273
A
LYS
22
G
ILE
284
A
ILE
33
G
ARG
298
A
ARG
47
G
ILE
443
A
ILE
152
G
ARG
456
A
ARG
165
G
GLU
466
A
GLU
175
G
PRO
470
A
PRO
179
G
ILE
359
A
ILE
81
G
PHE
361
A
PHE
83
G
SER
393
A
SER
115
G
TRP
395
A
TRP
117
H
VAL
5
B
VAL
5
H
GLN
6
B
GLN
6
H
VAL
18
B
VAL
18
H
TRP
23
B
TRP
23
H
THR
77
B
THR
80
H
ILE
82
B
ILE
85
H
VAL
67
B
VAL
70
H
ASP
72
B
ASP
75
H
GLY
10
B
GLY
10
H
LYS
12
B
LYS
12
H
THR
107
B
THR
119
H
VAL
111
B
VAL
123
H
ALA
88
B
ALA
94
H
LYS
96
B
LYS
102
H
THR
32
B
THR
32
H
GLN
39
B
GLN
40
H
GLU
46
B
GLU
47
H
LYS
52
B
LYS
53
H
VAL
56
B
VAL
59
H
PHE
58
B
PHE
61
H
GLY
10
B
GLY
10
H
LYS
12
B
LYS
12
H
THR
107
B
THR
119
H
VAL
111
B
VAL
123
H
ALA
88
B
ALA
94
H
LYS
96
B
LYS
102
H
PHE
100
B
PHE
112
H
TRP
103
B
TRP
115
F
H
SER
120
B
SER
132
H
LEU
124
B
LEU
136
H
THR
135
B
THR
147
H
TYR
145
B
TYR
157
H
TYR
176
B
TYR
188
H
PRO
185
B
PRO
197
H
VAL
163
B
VAL
175
H
THR
165
B
THR
177
H
SER
120
B
SER
132
H
LEU
124
B
LEU
136
H
THR
135
B
THR
147
H
TYR
145
B
TYR
157
H
TYR
176
B
TYR
188
H
PRO
185
B
PRO
197
H
VAL
169
B
VAL
181
H
LEU
170
B
LEU
182
H
THR
151
B
THR
163
H
TRP
154
B
TRP
166
H
TYR
194
B
TYR
206
H
HIS
200
B
HIS
212
H
THR
205
B
THR
217
H
VAL
211
B
VAL
223
L
THR
5
C
THR
5
L
SER
7
C
SER
7
L
ALA
19
C
ALA
19
L
THR
24
C
THR
24
L
GLN
70
C
GLN
68
L
ILE
75
C
ILE
73
L
PHE
62
C
PHE
60
L
PHE
67
C
PHE
65
L
THR
10
C
THR
10
L
LEU
13
C
LEU
13
L
THR
102
C
THR
96
L
ILE
106
C
ILE
100
L
ARG
85
C
ARG
83
L
GLN
90
C
GLN
88
L
THR
34
C
THR
32
L
LYS
38
C
LYS
36
L
LYS
45
C
LYS
43
L
PHE
49
C
PHE
47
L
LYS
53
C
LYS
51
L
ARG
54
C
ARG
52
L
THR
10
C
THR
10
L
LEU
13
C
LEU
13
L
THR
102
C
THR
96
L
ILE
106
C
ILE
100
L
ARG
85
C
ARG
83
L
GLN
90
C
GLN
88
L
PHE
97
C
PHE
91
L
PHE
98
C
PHE
92
L
SER
114
C
SER
108
L
PHE
118
C
PHE
112
L
THR
129
C
THR
123
L
PHE
139
C
PHE
133
L
TYR
173
C
TYR
167
L
SER
182
C
SER
176
L
SER
159
C
SER
153
L
VAL
163
C
VAL
157
L
LEU
154
C
LEU
148
L
GLN
155
C
GLN
149
L
ALA
144
C
ALA
138
L
VAL
150
C
VAL
144
L
VAL
191
C
VAL
185
L
HIS
198
C
HIS
192
L
VAL
205
C
VAL
199
L
ASN
210
C
ASN
204
BINDING SITE FOR RESIDUE CA L 301
L
CA
301
Software
2
L
GLU
105
C
GLU
99
2
1_555
L
GLU
143
C
GLU
137
2
1_555
4
P 1 21 1