0.015734
0.000000
0.000000
0.000000
0.014938
0.000000
0.000000
0.000000
0.011360
0.00000
0.00000
0.00000
Kwon, Y.D.
Kwong, P.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
63.556
66.944
88.029
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
C8 H18 N2 O4 S
238.305
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
non-polymer
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
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
D-saccharide, beta 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
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
109
5663
5668
10.1073/pnas.1112391109
22451932
Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops.
2012
100
1
IMAGE PLATE
2010-07-16
MAR scanner 300 mm plate
SINGLE WAVELENGTH
M
x-ray
1
1
1.0
22-BM
APS
1
SYNCHROTRON
APS BEAMLINE 22-BM
39211.434
HIV-1 clade A/E 93TH057 gp120
1
man
polymer
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
10
man
non-polymer
238.305
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
1
syn
non-polymer
18.015
water
148
nat
water
no
no
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLT
GGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSEN
LTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM
HHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGG
ANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLT
GGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSEN
LTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM
HHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGG
ANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
HIV-1
sample
HIV-1 env
11676
Human immunodeficiency virus 1
HEK 293
9606
HOMO SAPIENS
plasmid
pVRC8400
1
2.39
48.49
VAPOR DIFFUSION, HANGING DROP
7.5
14% PEG 1500, 12% PEG 400, 0.1M HEPES, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5
293
software
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
struct_conn
struct_site
struct_site_gen
repository
Initial release
Carbohydrate remediation
repository
Remediation
Database references
Refinement description
Data collection
Derived calculations
Structure summary
1
0
2012-04-04
1
1
2012-05-23
1
2
2017-11-08
1
3
2020-07-29
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_role
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
RCSB
Y
RCSB
2011-08-17
REL
REL
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
EPE
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HOH
water
NAG
734
2
NAG
NAG
734
A
NAG
741
2
NAG
NAG
741
A
NAG
762
2
NAG
NAG
762
A
NAG
776
2
NAG
NAG
776
A
NAG
789
2
NAG
NAG
789
A
NAG
795
2
NAG
NAG
795
A
NAG
834
2
NAG
NAG
834
A
NAG
886
2
NAG
NAG
886
A
NAG
892
2
NAG
NAG
892
A
NAG
948
2
NAG
NAG
948
A
EPE
1
3
EPE
EPE
1
A
HOH
2
4
HOH
HOH
2
A
HOH
3
4
HOH
HOH
3
A
HOH
4
4
HOH
HOH
4
A
HOH
5
4
HOH
HOH
5
A
HOH
6
4
HOH
HOH
6
A
HOH
7
4
HOH
HOH
7
A
HOH
8
4
HOH
HOH
8
A
HOH
9
4
HOH
HOH
9
A
HOH
10
4
HOH
HOH
10
A
HOH
11
4
HOH
HOH
11
A
HOH
12
4
HOH
HOH
12
A
HOH
13
4
HOH
HOH
13
A
HOH
14
4
HOH
HOH
14
A
HOH
15
4
HOH
HOH
15
A
HOH
16
4
HOH
HOH
16
A
HOH
17
4
HOH
HOH
17
A
HOH
18
4
HOH
HOH
18
A
HOH
19
4
HOH
HOH
19
A
HOH
20
4
HOH
HOH
20
A
HOH
21
4
HOH
HOH
21
A
HOH
22
4
HOH
HOH
22
A
HOH
23
4
HOH
HOH
23
A
HOH
24
4
HOH
HOH
24
A
HOH
25
4
HOH
HOH
25
A
HOH
26
4
HOH
HOH
26
A
HOH
27
4
HOH
HOH
27
A
HOH
28
4
HOH
HOH
28
A
HOH
29
4
HOH
HOH
29
A
HOH
30
4
HOH
HOH
30
A
HOH
31
4
HOH
HOH
31
A
HOH
32
4
HOH
HOH
32
A
HOH
33
4
HOH
HOH
33
A
HOH
34
4
HOH
HOH
34
A
HOH
35
4
HOH
HOH
35
A
HOH
36
4
HOH
HOH
36
A
HOH
37
4
HOH
HOH
37
A
HOH
38
4
HOH
HOH
38
A
HOH
39
4
HOH
HOH
39
A
HOH
40
4
HOH
HOH
40
A
HOH
41
4
HOH
HOH
41
A
HOH
42
4
HOH
HOH
42
A
HOH
43
4
HOH
HOH
43
A
HOH
125
4
HOH
HOH
125
A
HOH
126
4
HOH
HOH
126
A
HOH
127
4
HOH
HOH
127
A
HOH
128
4
HOH
HOH
128
A
HOH
129
4
HOH
HOH
129
A
HOH
130
4
HOH
HOH
130
A
HOH
131
4
HOH
HOH
131
A
HOH
132
4
HOH
HOH
132
A
HOH
133
4
HOH
HOH
133
A
HOH
134
4
HOH
HOH
134
A
HOH
135
4
HOH
HOH
135
A
HOH
136
4
HOH
HOH
136
A
HOH
137
4
HOH
HOH
137
A
HOH
138
4
HOH
HOH
138
A
HOH
139
4
HOH
HOH
139
A
HOH
140
4
HOH
HOH
140
A
HOH
141
4
HOH
HOH
141
A
HOH
142
4
HOH
HOH
142
A
HOH
143
4
HOH
HOH
143
A
HOH
144
4
HOH
HOH
144
A
HOH
145
4
HOH
HOH
145
A
HOH
146
4
HOH
HOH
146
A
HOH
147
4
HOH
HOH
147
A
HOH
148
4
HOH
HOH
148
A
HOH
1
4
HOH
HOH
493
A
HOH
44
4
HOH
HOH
494
A
HOH
45
4
HOH
HOH
495
A
HOH
46
4
HOH
HOH
496
A
HOH
47
4
HOH
HOH
497
A
HOH
48
4
HOH
HOH
498
A
HOH
49
4
HOH
HOH
499
A
HOH
50
4
HOH
HOH
500
A
HOH
51
4
HOH
HOH
501
A
HOH
52
4
HOH
HOH
502
A
HOH
53
4
HOH
HOH
503
A
HOH
54
4
HOH
HOH
504
A
HOH
55
4
HOH
HOH
505
A
HOH
56
4
HOH
HOH
506
A
HOH
57
4
HOH
HOH
507
A
HOH
58
4
HOH
HOH
508
A
HOH
59
4
HOH
HOH
509
A
HOH
60
4
HOH
HOH
510
A
HOH
61
4
HOH
HOH
511
A
HOH
62
4
HOH
HOH
512
A
HOH
63
4
HOH
HOH
513
A
HOH
64
4
HOH
HOH
514
A
HOH
65
4
HOH
HOH
515
A
HOH
66
4
HOH
HOH
516
A
HOH
67
4
HOH
HOH
517
A
HOH
68
4
HOH
HOH
518
A
HOH
69
4
HOH
HOH
519
A
HOH
70
4
HOH
HOH
520
A
HOH
71
4
HOH
HOH
521
A
HOH
72
4
HOH
HOH
522
A
HOH
73
4
HOH
HOH
523
A
HOH
74
4
HOH
HOH
524
A
HOH
75
4
HOH
HOH
525
A
HOH
76
4
HOH
HOH
526
A
HOH
77
4
HOH
HOH
527
A
HOH
78
4
HOH
HOH
528
A
HOH
79
4
HOH
HOH
529
A
HOH
80
4
HOH
HOH
530
A
HOH
81
4
HOH
HOH
531
A
HOH
82
4
HOH
HOH
532
A
HOH
83
4
HOH
HOH
533
A
HOH
84
4
HOH
HOH
534
A
HOH
85
4
HOH
HOH
535
A
HOH
86
4
HOH
HOH
536
A
HOH
87
4
HOH
HOH
537
A
HOH
88
4
HOH
HOH
538
A
HOH
89
4
HOH
HOH
539
A
HOH
90
4
HOH
HOH
540
A
HOH
91
4
HOH
HOH
541
A
HOH
92
4
HOH
HOH
542
A
HOH
93
4
HOH
HOH
543
A
HOH
94
4
HOH
HOH
544
A
HOH
95
4
HOH
HOH
545
A
HOH
96
4
HOH
HOH
546
A
HOH
97
4
HOH
HOH
547
A
HOH
98
4
HOH
HOH
548
A
HOH
99
4
HOH
HOH
549
A
HOH
100
4
HOH
HOH
550
A
HOH
101
4
HOH
HOH
551
A
HOH
102
4
HOH
HOH
552
A
HOH
103
4
HOH
HOH
553
A
HOH
104
4
HOH
HOH
554
A
HOH
105
4
HOH
HOH
555
A
HOH
106
4
HOH
HOH
556
A
HOH
107
4
HOH
HOH
557
A
HOH
108
4
HOH
HOH
558
A
HOH
109
4
HOH
HOH
559
A
HOH
110
4
HOH
HOH
560
A
HOH
111
4
HOH
HOH
561
A
HOH
112
4
HOH
HOH
562
A
HOH
113
4
HOH
HOH
563
A
HOH
114
4
HOH
HOH
564
A
HOH
115
4
HOH
HOH
565
A
HOH
116
4
HOH
HOH
566
A
HOH
117
4
HOH
HOH
567
A
HOH
118
4
HOH
HOH
568
A
HOH
119
4
HOH
HOH
569
A
HOH
120
4
HOH
HOH
570
A
HOH
121
4
HOH
HOH
571
A
HOH
122
4
HOH
HOH
572
A
HOH
123
4
HOH
HOH
573
A
HOH
124
4
HOH
HOH
574
A
VAL
44
n
1
VAL
44
A
TRP
45
n
2
TRP
45
A
LYS
46
n
3
LYS
46
A
ASP
47
n
4
ASP
47
A
ALA
48
n
5
ALA
48
A
ASP
49
n
6
ASP
49
A
THR
50
n
7
THR
50
A
THR
51
n
8
THR
51
A
LEU
52
n
9
LEU
52
A
PHE
53
n
10
PHE
53
A
CYS
54
n
11
CYS
54
A
ALA
55
n
12
ALA
55
A
SER
56
n
13
SER
56
A
ASP
57
n
14
ASP
57
A
ALA
58
n
15
ALA
58
A
LYS
59
n
16
LYS
59
A
ALA
60
n
17
ALA
60
A
HIS
61
n
18
HIS
61
A
GLU
62
n
19
GLU
62
A
THR
63
n
20
THR
63
A
GLU
64
n
21
GLU
64
A
VAL
65
n
22
VAL
65
A
HIS
66
n
23
HIS
66
A
ASN
67
n
24
ASN
67
A
VAL
68
n
25
VAL
68
A
TRP
69
n
26
TRP
69
A
ALA
70
n
27
ALA
70
A
THR
71
n
28
THR
71
A
HIS
72
n
29
HIS
72
A
ALA
73
n
30
ALA
73
A
CYS
74
n
31
CYS
74
A
VAL
75
n
32
VAL
75
A
PRO
76
n
33
PRO
76
A
THR
77
n
34
THR
77
A
ASP
78
n
35
ASP
78
A
PRO
79
n
36
PRO
79
A
ASN
80
n
37
ASN
80
A
PRO
81
n
38
PRO
81
A
GLN
82
n
39
GLN
82
A
GLU
83
n
40
GLU
83
A
ILE
84
n
41
ILE
84
A
HIS
85
n
42
HIS
85
A
LEU
86
n
43
LEU
86
A
GLU
87
n
44
GLU
87
A
ASN
88
n
45
ASN
88
A
VAL
89
n
46
VAL
89
A
THR
90
n
47
THR
90
A
GLU
91
n
48
GLU
91
A
ASN
92
n
49
ASN
92
A
PHE
93
n
50
PHE
93
A
ASN
94
n
51
ASN
94
A
MET
95
n
52
MET
95
A
TRP
96
n
53
TRP
96
A
LYS
97
n
54
LYS
97
A
ASN
98
n
55
ASN
98
A
ASN
99
n
56
ASN
99
A
MET
100
n
57
MET
100
A
VAL
101
n
58
VAL
101
A
GLU
102
n
59
GLU
102
A
GLN
103
n
60
GLN
103
A
MET
104
n
61
MET
104
A
GLN
105
n
62
GLN
105
A
GLU
106
n
63
GLU
106
A
ASP
107
n
64
ASP
107
A
VAL
108
n
65
VAL
108
A
ILE
109
n
66
ILE
109
A
SER
110
n
67
SER
110
A
LEU
111
n
68
LEU
111
A
TRP
112
n
69
TRP
112
A
ASP
113
n
70
ASP
113
A
GLN
114
n
71
GLN
114
A
SER
115
n
72
SER
115
A
LEU
116
n
73
LEU
116
A
GLN
117
n
74
GLN
117
A
PRO
118
n
75
PRO
118
A
CYS
119
n
76
CYS
119
A
VAL
120
n
77
VAL
120
A
LYS
121
n
78
LYS
121
A
LEU
122
n
79
LEU
122
A
THR
123
n
80
THR
123
A
GLY
124
n
81
GLY
124
A
GLY
198
n
82
GLY
198
A
SER
199
n
83
SER
199
A
VAL
200
n
84
VAL
200
A
ILE
201
n
85
ILE
201
A
LYS
202
n
86
LYS
202
A
GLN
203
n
87
GLN
203
A
ALA
204
n
88
ALA
204
A
CYS
205
n
89
CYS
205
A
PRO
206
n
90
PRO
206
A
LYS
207
n
91
LYS
207
A
ILE
208
n
92
ILE
208
A
SER
209
n
93
SER
209
A
PHE
210
n
94
PHE
210
A
ASP
211
n
95
ASP
211
A
PRO
212
n
96
PRO
212
A
ILE
213
n
97
ILE
213
A
PRO
214
n
98
PRO
214
A
ILE
215
n
99
ILE
215
A
HIS
216
n
100
HIS
216
A
TYR
217
n
101
TYR
217
A
CYS
218
n
102
CYS
218
A
THR
219
n
103
THR
219
A
PRO
220
n
104
PRO
220
A
ALA
221
n
105
ALA
221
A
GLY
222
n
106
GLY
222
A
TYR
223
n
107
TYR
223
A
VAL
224
n
108
VAL
224
A
ILE
225
n
109
ILE
225
A
LEU
226
n
110
LEU
226
A
LYS
227
n
111
LYS
227
A
CYS
228
n
112
CYS
228
A
ASN
229
n
113
ASN
229
A
ASP
230
n
114
ASP
230
A
LYS
231
n
115
LYS
231
A
ASN
232
n
116
ASN
232
A
PHE
233
n
117
PHE
233
A
ASN
234
n
118
ASN
234
A
GLY
235
n
119
GLY
235
A
THR
236
n
120
THR
236
A
GLY
237
n
121
GLY
237
A
PRO
238
n
122
PRO
238
A
CYS
239
n
123
CYS
239
A
LYS
240
n
124
LYS
240
A
ASN
241
n
125
ASN
241
A
VAL
242
n
126
VAL
242
A
SER
243
n
127
SER
243
A
SER
244
n
128
SER
244
A
VAL
245
n
129
VAL
245
A
GLN
246
n
130
GLN
246
A
CYS
247
n
131
CYS
247
A
THR
248
n
132
THR
248
A
HIS
249
n
133
HIS
249
A
GLY
250
n
134
GLY
250
A
ILE
251
n
135
ILE
251
A
LYS
252
n
136
LYS
252
A
PRO
253
n
137
PRO
253
A
VAL
254
n
138
VAL
254
A
VAL
255
n
139
VAL
255
A
SER
256
n
140
SER
256
A
THR
257
n
141
THR
257
A
GLN
258
n
142
GLN
258
A
LEU
259
n
143
LEU
259
A
LEU
260
n
144
LEU
260
A
LEU
261
n
145
LEU
261
A
ASN
262
n
146
ASN
262
A
GLY
263
n
147
GLY
263
A
SER
264
n
148
SER
264
A
LEU
265
n
149
LEU
265
A
ALA
266
n
150
ALA
266
A
GLU
267
n
151
GLU
267
A
GLU
268
n
152
GLU
268
A
GLU
269
n
153
GLU
269
A
ILE
270
n
154
ILE
270
A
ILE
271
n
155
ILE
271
A
ILE
272
n
156
ILE
272
A
ARG
273
n
157
ARG
273
A
SER
274
n
158
SER
274
A
GLU
275
n
159
GLU
275
A
ASN
276
n
160
ASN
276
A
LEU
277
n
161
LEU
277
A
THR
278
n
162
THR
278
A
ASN
279
n
163
ASN
279
A
ASN
280
n
164
ASN
280
A
ALA
281
n
165
ALA
281
A
LYS
282
n
166
LYS
282
A
THR
283
n
167
THR
283
A
ILE
284
n
168
ILE
284
A
ILE
285
n
169
ILE
285
A
VAL
286
n
170
VAL
286
A
HIS
287
n
171
HIS
287
A
LEU
288
n
172
LEU
288
A
ASN
289
n
173
ASN
289
A
LYS
290
n
174
LYS
290
A
SER
291
n
175
SER
291
A
VAL
292
n
176
VAL
292
A
GLU
293
n
177
GLU
293
A
ILE
294
n
178
ILE
294
A
ASN
295
n
179
ASN
295
A
CYS
296
n
180
CYS
296
A
THR
297
n
181
THR
297
A
ARG
298
n
182
ARG
298
A
PRO
299
n
183
PRO
299
A
SER
300
n
184
SER
300
A
ASN
301
n
185
ASN
301
A
n
186
318
A
n
187
319
A
n
188
320
A
n
189
321
A
n
190
322
A
n
191
323
A
GLY
324
n
192
GLY
324
A
ASP
325
n
193
ASP
325
A
ILE
326
n
194
ILE
326
A
ARG
327
n
195
ARG
327
A
LYS
328
n
196
LYS
328
A
ALA
329
n
197
ALA
329
A
TYR
330
n
198
TYR
330
A
CYS
331
n
199
CYS
331
A
GLU
332
n
200
GLU
332
A
ILE
333
n
201
ILE
333
A
ASN
334
n
202
ASN
334
A
GLY
335
n
203
GLY
335
A
THR
336
n
204
THR
336
A
LYS
337
n
205
LYS
337
A
TRP
338
n
206
TRP
338
A
ASN
339
n
207
ASN
339
A
LYS
340
n
208
LYS
340
A
VAL
341
n
209
VAL
341
A
LEU
342
n
210
LEU
342
A
LYS
343
n
211
LYS
343
A
GLN
344
n
212
GLN
344
A
VAL
345
n
213
VAL
345
A
THR
346
n
214
THR
346
A
GLU
347
n
215
GLU
347
A
LYS
348
n
216
LYS
348
A
LEU
349
n
217
LEU
349
A
LYS
350
n
218
LYS
350
A
GLU
351
n
219
GLU
351
A
HIS
352
n
220
HIS
352
A
PHE
353
n
221
PHE
353
A
ASN
354
n
222
ASN
354
A
ASN
355
n
223
ASN
355
A
LYS
357
n
224
LYS
357
A
THR
358
n
225
THR
358
A
ILE
359
n
226
ILE
359
A
ILE
360
n
227
ILE
360
A
PHE
361
n
228
PHE
361
A
GLN
362
n
229
GLN
362
A
PRO
363
n
230
PRO
363
A
PRO
364
n
231
PRO
364
A
SER
365
n
232
SER
365
A
GLY
366
n
233
GLY
366
A
GLY
367
n
234
GLY
367
A
ASP
368
n
235
ASP
368
A
LEU
369
n
236
LEU
369
A
GLU
370
n
237
GLU
370
A
ILE
371
n
238
ILE
371
A
THR
372
n
239
THR
372
A
MET
373
n
240
MET
373
A
HIS
374
n
241
HIS
374
A
HIS
375
n
242
HIS
375
A
PHE
376
n
243
PHE
376
A
ASN
377
n
244
ASN
377
A
CYS
378
n
245
CYS
378
A
ARG
379
n
246
ARG
379
A
GLY
380
n
247
GLY
380
A
GLU
381
n
248
GLU
381
A
PHE
382
n
249
PHE
382
A
PHE
383
n
250
PHE
383
A
TYR
384
n
251
TYR
384
A
CYS
385
n
252
CYS
385
A
ASN
386
n
253
ASN
386
A
THR
387
n
254
THR
387
A
THR
388
n
255
THR
388
A
GLN
389
n
256
GLN
389
A
LEU
390
n
257
LEU
390
A
PHE
391
n
258
PHE
391
A
ASN
392
n
259
ASN
392
A
ASN
393
n
260
ASN
393
A
THR
394
n
261
THR
394
A
CYS
395
n
262
CYS
395
A
ILE
396
n
263
ILE
396
A
n
264
403
A
n
265
404
A
n
266
405
A
n
267
406
A
n
268
407
A
LYS
408
n
269
LYS
408
A
GLY
409
n
270
GLY
409
A
CYS
410
n
271
CYS
410
A
ASN
411
n
272
ASN
411
A
GLY
412
n
273
GLY
412
A
THR
413
n
274
THR
413
A
ILE
414
n
275
ILE
414
A
THR
415
n
276
THR
415
A
LEU
416
n
277
LEU
416
A
PRO
417
n
278
PRO
417
A
CYS
418
n
279
CYS
418
A
LYS
419
n
280
LYS
419
A
ILE
420
n
281
ILE
420
A
LYS
421
n
282
LYS
421
A
GLN
422
n
283
GLN
422
A
ILE
423
n
284
ILE
423
A
ILE
424
n
285
ILE
424
A
ASN
425
n
286
ASN
425
A
MET
426
n
287
MET
426
A
TRP
427
n
288
TRP
427
A
GLN
428
n
289
GLN
428
A
GLY
429
n
290
GLY
429
A
THR
430
n
291
THR
430
A
GLY
431
n
292
GLY
431
A
GLN
432
n
293
GLN
432
A
ALA
433
n
294
ALA
433
A
MET
434
n
295
MET
434
A
TYR
435
n
296
TYR
435
A
ALA
436
n
297
ALA
436
A
PRO
437
n
298
PRO
437
A
PRO
438
n
299
PRO
438
A
ILE
439
n
300
ILE
439
A
ASP
440
n
301
ASP
440
A
GLY
441
n
302
GLY
441
A
LYS
442
n
303
LYS
442
A
ILE
443
n
304
ILE
443
A
ASN
444
n
305
ASN
444
A
CYS
445
n
306
CYS
445
A
VAL
446
n
307
VAL
446
A
SER
447
n
308
SER
447
A
ASN
448
n
309
ASN
448
A
ILE
449
n
310
ILE
449
A
THR
450
n
311
THR
450
A
GLY
451
n
312
GLY
451
A
ILE
452
n
313
ILE
452
A
LEU
453
n
314
LEU
453
A
LEU
454
n
315
LEU
454
A
THR
455
n
316
THR
455
A
ARG
456
n
317
ARG
456
A
ASP
457
n
318
ASP
457
A
GLY
458
n
319
GLY
458
A
GLY
459
n
320
GLY
459
A
ALA
460
n
321
ALA
460
A
ASN
461
n
322
ASN
461
A
ASN
462
n
323
ASN
462
A
THR
463
n
324
THR
463
A
SER
464
n
325
SER
464
A
ASN
465
n
326
ASN
465
A
GLU
466
n
327
GLU
466
A
THR
467
n
328
THR
467
A
PHE
468
n
329
PHE
468
A
ARG
469
n
330
ARG
469
A
PRO
470
n
331
PRO
470
A
GLY
471
n
332
GLY
471
A
GLY
472
n
333
GLY
472
A
GLY
473
n
334
GLY
473
A
ASN
474
n
335
ASN
474
A
ILE
475
n
336
ILE
475
A
LYS
476
n
337
LYS
476
A
ASP
477
n
338
ASP
477
A
ASN
478
n
339
ASN
478
A
TRP
479
n
340
TRP
479
A
ARG
480
n
341
ARG
480
A
SER
481
n
342
SER
481
A
GLU
482
n
343
GLU
482
A
LEU
483
n
344
LEU
483
A
TYR
484
n
345
TYR
484
A
LYS
485
n
346
LYS
485
A
TYR
486
n
347
TYR
486
A
LYS
487
n
348
LYS
487
A
VAL
488
n
349
VAL
488
A
VAL
489
n
350
VAL
489
A
GLN
490
n
351
GLN
490
A
ILE
491
n
352
ILE
491
A
GLU
492
n
353
GLU
492
A
1.3719
0.0160
-0.9221
0.8971
-0.5505
0.8850
-0.0685
-0.1073
0.3159
-0.1386
0.0355
-0.0473
-0.4479
0.3098
0.0401
0.4241
-0.0748
-0.0077
0.3251
0.0066
0.2948
refined
15.7912
7.5291
-18.3549
X-RAY DIFFRACTION
1.3780
0.6429
0.7281
2.4082
0.9575
2.4516
-0.1086
-0.1682
0.1367
0.0236
-0.0019
0.1441
-0.1841
0.0563
0.0820
0.2575
-0.0231
0.0274
0.2436
0.0108
0.2280
refined
11.6296
-1.6387
-13.8940
X-RAY DIFFRACTION
1.8624
0.3582
1.2056
2.1698
0.5581
2.9239
0.0584
0.1011
-0.2977
0.1776
0.1187
-0.2488
0.3329
0.2811
-0.1788
0.2850
0.0524
0.0071
0.2674
-0.0256
0.3199
refined
15.9172
-21.2629
-15.1480
X-RAY DIFFRACTION
0.5689
-0.4296
0.0995
1.4921
-0.4937
0.2340
-0.1333
-0.3578
0.0285
0.2787
0.1294
-0.0060
-0.0038
0.1200
-0.0069
0.2943
-0.0358
-0.0195
0.3541
-0.0152
0.2599
refined
16.6589
0.2471
-7.9503
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
chain A and resi 44:89
X-RAY DIFFRACTION
2
chain A and resi 90:254
X-RAY DIFFRACTION
3
chain A and resi 255:474
X-RAY DIFFRACTION
4
chain A and resi 475:492
author_and_software_defined_assembly
PISA
1
monomeric
A
ASN
234
GLYCOSYLATION SITE
A
ASN
118
ASN
A
ASN
334
GLYCOSYLATION SITE
A
ASN
202
ASN
A
ASN
386
GLYCOSYLATION SITE
A
ASN
253
ASN
A
ASN
448
GLYCOSYLATION SITE
A
ASN
309
ASN
A
ASN
289
GLYCOSYLATION SITE
A
ASN
173
ASN
A
ASN
241
GLYCOSYLATION SITE
A
ASN
125
ASN
A
ASN
262
GLYCOSYLATION SITE
A
ASN
146
ASN
A
ASN
295
GLYCOSYLATION SITE
A
ASN
179
ASN
A
ASN
392
GLYCOSYLATION SITE
A
ASN
259
ASN
A
ASN
276
GLYCOSYLATION SITE
A
ASN
160
ASN
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
LYS
46
A
N
LYS
3
A
O
GLN
490
A
O
GLN
351
A
O
LYS
487
A
O
LYS
348
A
N
LEU
226
A
N
LEU
110
A
N
LYS
227
A
N
LYS
111
A
O
SER
243
A
O
SER
127
A
O
SER
244
A
O
SER
128
A
N
ILE
84
A
N
ILE
41
A
O
VAL
75
A
O
VAL
32
A
N
CYS
54
A
N
CYS
11
A
N
ALA
55
A
N
ALA
12
A
O
HIS
216
A
O
HIS
100
A
N
PHE
93
A
N
PHE
50
A
O
GLY
237
A
O
GLY
121
A
O
SER
199
A
O
SER
83
A
N
THR
123
A
N
THR
80
A
N
LEU
122
A
N
LEU
79
A
O
GLN
432
A
O
GLN
293
A
O
ALA
433
A
O
ALA
294
A
N
ILE
424
A
N
ILE
285
A
N
LEU
260
A
N
LEU
144
A
O
THR
450
A
O
THR
311
A
O
ILE
452
A
O
ILE
313
A
N
VAL
286
A
N
VAL
170
A
O
PHE
468
A
O
PHE
329
A
N
ILE
360
A
N
ILE
227
A
N
ILE
271
A
N
ILE
155
A
O
HIS
287
A
O
HIS
171
A
N
VAL
286
A
N
VAL
170
A
O
ILE
452
A
O
ILE
313
A
N
ILE
333
A
N
ILE
201
A
O
ILE
414
A
O
ILE
275
A
O
LYS
419
A
O
LYS
280
A
N
TYR
384
A
N
TYR
251
A
O
PHE
383
A
O
PHE
250
A
N
PHE
376
A
N
PHE
243
1
A
GLY
318
A
GLY
186
1
Y
1
A
GLY
319
A
GLY
187
1
Y
1
A
SER
320
A
SER
188
1
Y
1
A
GLY
321
A
GLY
189
1
Y
1
A
SER
322
A
SER
190
1
Y
1
A
GLY
323
A
GLY
191
1
Y
1
A
GLY
403
A
GLY
264
1
Y
1
A
ASN
404
A
ASN
265
1
Y
1
A
GLU
405
A
GLU
266
1
Y
1
A
THR
406
A
THR
267
1
Y
1
A
MET
407
A
MET
268
1
Y
1
A
A
O
O
HOH
HOH
565
566
1.92
1
A
A
O
O
HOH
HOH
135
567
2.00
1
A
A
ND2
O5
ASN
NAG
234
734
2.02
1
A
ASN
88
35.01
39.43
1
A
LEU
116
-112.54
66.07
1
A
ASP
211
-168.87
107.73
1
A
GLN
258
69.17
-59.25
1
A
GLU
268
-131.94
-99.50
1
A
ASN
276
-173.00
94.68
1
A
PHE
391
-108.48
61.19
1
A
ASN
474
-178.92
112.89
10.7220
-0.0000
-0.0000
-4.9969
-0.0000
-5.7251
0.2307
0.1890
0.1910
1.9
24.571
1437
31824
29250
4.91
91.91
1.000
1.000
0.24
1
0.11
MOLECULAR REPLACEMENT
23.44
0.90
1.11
ML
FLAT BULK SOLVENT MODEL
36.441
0.329
1.9
24.571
148
2980
155
0
2677
0.007
2921
1.198
3960
15.937
1105
0.069
462
0.004
492
0.2307
0.2349
1.9343
83
1817
61.00
0.2760
0.2176
2.0117
152
2475
84.00
0.3130
0.2093
2.1032
166
2717
92.00
0.2610
0.2029
2.2140
144
2814
94.00
0.2560
0.1970
2.3526
141
2858
95.00
0.2440
0.2037
2.5341
158
2896
97.00
0.2692
0.1966
2.7888
152
2953
98.00
0.2095
0.1973
3.1916
142
3038
99.00
0.2326
0.1776
4.0182
145
3055
99.00
0.1972
0.1747
24.5735
154
3190
99.00
1.9
50
3TGT
32465
30907
0.0
0.0
0.084
0.074
1
38.5
6.8
95.2
0.615
1.90
1.93
2.1
0.555
1
5.5
86.5
0.498
1.93
1.97
2.7
0.452
1
5.8
89.9
0.479
1.97
2.01
3.1
0.416
1
6.0
95.2
0.419
2.01
2.05
3.7
0.368
1
6.4
97.8
0.377
2.05
2.09
4.9
0.339
1
6.7
99.5
0.327
2.09
2.14
6.3
0.269
1
6.9
99.8
0.296
2.14
2.19
7.3
0.265
1
7.1
100.0
0.257
2.19
2.25
9.6
0.226
1
7.2
100.0
0.219
2.25
2.32
11.9
0.197
1
7.3
100.0
0.190
2.32
2.39
15.5
0.172
1
7.3
99.9
0.171
2.39
2.48
16.5
0.155
1
7.2
100.0
0.144
2.48
2.58
20.9
0.137
1
7.2
100.0
0.129
2.58
2.70
24.6
0.126
1
7.2
100.0
0.115
2.70
2.84
28.7
0.116
1
7.1
99.9
0.101
2.84
3.02
34.5
0.103
1
7.1
100.0
0.091
3.02
3.25
41.9
0.093
1
6.9
99.9
0.085
3.25
3.58
46.2
0.090
1
6.6
100.0
0.075
3.58
4.09
51.3
0.081
1
6.3
99.9
0.067
4.09
5.16
57.3
0.075
1
6.6
99.9
0.053
5.16
50.00
57.9
0.062
1
6.4
98.1
refinement
Paul D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
1.6.1_357
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
data reduction
DENZO
data scaling
SCALEPACK
HIV-1 clade A/E 93TH057 gp120
Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 gp120 core
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
2
N
N
3
N
N
4
N
N
A
GLU
64
A
GLU
21
HELX_P
A
CYS
74
A
CYS
31
1
1
11
A
ASN
98
A
ASN
55
HELX_P
A
LEU
116
A
LEU
73
1
2
19
A
GLY
335
A
GLY
203
HELX_P
A
PHE
353
A
PHE
221
1
3
19
A
ASP
368
A
ASP
235
HELX_P
A
MET
373
A
MET
240
1
4
6
A
THR
387
A
THR
254
HELX_P
A
ILE
396
A
ILE
263
5
5
10
A
GLY
459
A
GLY
320
HELX_P
A
THR
463
A
THR
324
5
6
5
A
ASN
474
A
ASN
335
HELX_P
A
TYR
484
A
TYR
345
1
7
11
disulf
2.058
A
CYS
54
A
SG
CYS
11
1_555
A
CYS
74
A
SG
CYS
31
1_555
disulf
2.031
A
CYS
119
A
SG
CYS
76
1_555
A
CYS
205
A
SG
CYS
89
1_555
disulf
2.045
A
CYS
218
A
SG
CYS
102
1_555
A
CYS
247
A
SG
CYS
131
1_555
disulf
2.079
A
CYS
228
A
SG
CYS
112
1_555
A
CYS
239
A
SG
CYS
123
1_555
disulf
2.047
A
CYS
296
A
SG
CYS
180
1_555
A
CYS
331
A
SG
CYS
199
1_555
disulf
2.029
A
CYS
378
A
SG
CYS
245
1_555
A
CYS
445
A
SG
CYS
306
1_555
disulf
2.036
A
CYS
385
A
SG
CYS
252
1_555
A
CYS
418
A
SG
CYS
279
1_555
disulf
2.034
A
CYS
395
A
SG
CYS
262
1_555
A
CYS
410
A
SG
CYS
271
1_555
covale
1.309
one
N-Glycosylation
A
ASN
234
A
ND2
ASN
118
1_555
A
NAG
734
B
C1
NAG
1_555
covale
1.446
one
N-Glycosylation
A
ASN
241
A
ND2
ASN
125
1_555
A
NAG
741
C
C1
NAG
1_555
covale
1.448
one
N-Glycosylation
A
ASN
262
A
ND2
ASN
146
1_555
A
NAG
762
D
C1
NAG
1_555
covale
1.491
one
N-Glycosylation
A
ASN
276
A
ND2
ASN
160
1_555
A
NAG
776
E
C1
NAG
1_555
covale
1.445
one
N-Glycosylation
A
ASN
289
A
ND2
ASN
173
1_555
A
NAG
789
F
C1
NAG
1_555
covale
1.449
one
N-Glycosylation
A
ASN
295
A
ND2
ASN
179
1_555
A
NAG
795
G
C1
NAG
1_555
covale
1.434
one
N-Glycosylation
A
ASN
334
A
ND2
ASN
202
1_555
A
NAG
834
H
C1
NAG
1_555
covale
1.436
one
N-Glycosylation
A
ASN
386
A
ND2
ASN
253
1_555
A
NAG
886
I
C1
NAG
1_555
covale
1.451
one
N-Glycosylation
A
ASN
392
A
ND2
ASN
259
1_555
A
NAG
892
J
C1
NAG
1_555
covale
1.437
one
N-Glycosylation
A
ASN
448
A
ND2
ASN
309
1_555
A
NAG
948
K
C1
NAG
1_555
VIRAL PROTEIN
HIV-1 gp120, unliganded structure, clade A/E 93TH057, VIRAL PROTEIN
3TGT
PDB
1
3TGT
44
492
3TGT
44
492
3TGT
A
1
1
353
5
3
2
4
5
7
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TRP
45
A
TRP
2
A
ASP
47
A
ASP
4
A
TYR
486
A
TYR
347
A
ILE
491
A
ILE
352
A
TYR
223
A
TYR
107
A
CYS
228
A
CYS
112
A
VAL
242
A
VAL
126
A
VAL
245
A
VAL
129
A
GLU
83
A
GLU
40
A
HIS
85
A
HIS
42
A
VAL
75
A
VAL
32
A
PRO
76
A
PRO
33
A
PHE
53
A
PHE
10
A
SER
56
A
SER
13
A
HIS
216
A
HIS
100
A
CYS
218
A
CYS
102
A
GLU
91
A
GLU
48
A
ASN
94
A
ASN
51
A
THR
236
A
THR
120
A
CYS
239
A
CYS
123
A
SER
199
A
SER
83
A
LYS
202
A
LYS
86
A
VAL
120
A
VAL
77
A
THR
123
A
THR
80
A
GLN
432
A
GLN
293
A
MET
434
A
MET
295
A
ILE
423
A
ILE
284
A
ASN
425
A
ASN
286
A
LEU
259
A
LEU
143
A
LEU
261
A
LEU
145
A
ILE
443
A
ILE
304
A
ARG
456
A
ARG
317
A
ILE
284
A
ILE
168
A
ARG
298
A
ARG
182
A
ASN
465
A
ASN
326
A
PRO
470
A
PRO
331
A
THR
358
A
THR
225
A
PHE
361
A
PHE
228
A
ILE
271
A
ILE
155
A
ARG
273
A
ARG
157
A
ILE
284
A
ILE
168
A
ARG
298
A
ARG
182
A
ILE
443
A
ILE
304
A
ARG
456
A
ARG
317
A
LYS
328
A
LYS
196
A
ASN
334
A
ASN
202
A
THR
413
A
THR
274
A
ILE
420
A
ILE
281
A
GLU
381
A
GLU
248
A
CYS
385
A
CYS
252
A
HIS
374
A
HIS
241
A
CYS
378
A
CYS
245
19
P 21 21 21