0.011148
0.000000
0.000000
0.000000
0.006494
0.000000
0.000000
0.000000
0.008203
0.00000
0.00000
0.00000
CIS PROLINE - PRO L 8
CIS PROLINE - PRO L 77
CIS PROLINE - PRO L 95
CIS PROLINE - PRO L 141
CIS PROLINE - PRO H 149
CIS PROLINE - PRO H 151
CIS PROLINE - PRO H 200
Ghiara, J.B.
Wilson, I.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
89.700
154.000
121.900
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
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
US
Science
SCIEAS
0038
0036-8075
264
82
85
7511253
Crystal structure of the principal neutralization site of HIV-1.
1994
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
x-ray
1
1.0
23675.107
IGG1-KAPPA 59.1 FAB (LIGHT CHAIN)
1
man
polymer
24208.383
IGG1-KAPPA 59.1 FAB (HEAVY CHAIN)
1
man
polymer
2814.339
HIV-1 GP120 (MN ISOLATE)
FRAGMENT (RESIDUES 308 - 332)
1
man
polymer
no
no
DIVMTQSPASLVVSLGQRATISCRASESVDSYGKSFMHWYQQKPGQPPKVLIYIASNLESGVPARFSGSGSRTDFTLTID
PVEADDAATYYCQQNNEDPPTFGAGTKLEMRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQ
NGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR
DIVMTQSPASLVVSLGQRATISCRASESVDSYGKSFMHWYQQKPGQPPKVLIYIASNLESGVPARFSGSGSRTDFTLTID
PVEADDAATYYCQQNNEDPPTFGAGTKLEMRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQ
NGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR
L
polypeptide(L)
no
no
QVKLQESGPAVIKPSQSLSLTCIVSGFSITRTNYCWHWIRQAPGKGLEWMGRICYEGSIYYSPSIKSRSTISRDTSLNKF
FIQLISVTNEDTAMYYCSRENHMYETYFDVWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTV
TWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPR
QVKLQESGPAVIKPSQSLSLTCIVSGFSITRTNYCWHWIRQAPGKGLEWMGRICYEGSIYYSPSIKSRSTISRDTSLNKF
FIQLISVTNEDTAMYYCSRENHMYETYFDVWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTV
TWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPR
H
polypeptide(L)
no
no
YNKRKRIHIGPGRAFYTTKNIIGC
YNKRKRIHIGPGRAFYTTKNIIGC
P
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
house mouse
Mus
sample
10090
Mus musculus
house mouse
Mus
sample
10090
Mus musculus
Lentivirus
Human immunodeficiency virus 1
sample
11696
HIV-1 M:B_MN
4.15
70.36
repository
Initial release
Version format compliance
Version format compliance
1
0
1994-07-31
1
1
2008-03-25
1
2
2011-07-13
Y
1994-02-10
REL
THE PEPTIDE USED WAS A SYNTHETIC HOMOLOGUE OF RESIDUES 308
- 332 OF HIV-1 GP120 (MN STRAIN), WITH AN ADDITIONAL CYS AT
THE C-TERMINAL END.
THE FAB FRAGMENT IS NUMBERED ACCORDING TO THE CONVENTION OF
E. KABAT (E.A. KABAT, T.T. WU, M. REID-MILLER, H.M. PERRY,
K.S. GOTTESMAN, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL
INTEREST, 4TH ED., (1987), NATIONAL INSTITUTE OF HEALTH,
BETHESDA, MD.
THE PEPTIDE IS NUMBERED ACCORDING TO THE BH10 ISOLATE
SEQUENCE (L. RATNER, W. HASELTINE, R. PATARCA, K.J. LIVAK,
B. STARCICH, S.F. JOSEPHS, E.R. DORAN, J.A. RAFALSKI, E.A.
WHITEHORN, K. BAUMEISTER, L. IVANOFF, S.R. PETTEWAY JR.,
M.L. PEARSON, J.A. LAUTENBERGER, T.S. PAPAS, J. GHRAYEB,
N.T. CHANG, R.C. GALLO, F. WONG-STAAL (1985) NATURE V. 313,
277-284.)
ASP
1
n
1
ASP
1
L
ILE
2
n
2
ILE
2
L
VAL
3
n
3
VAL
3
L
MET
4
n
4
MET
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
ALA
9
n
9
ALA
9
L
SER
10
n
10
SER
10
L
LEU
11
n
11
LEU
11
L
VAL
12
n
12
VAL
12
L
VAL
13
n
13
VAL
13
L
SER
14
n
14
SER
14
L
LEU
15
n
15
LEU
15
L
GLY
16
n
16
GLY
16
L
GLN
17
n
17
GLN
17
L
ARG
18
n
18
ARG
18
L
ALA
19
n
19
ALA
19
L
THR
20
n
20
THR
20
L
ILE
21
n
21
ILE
21
L
SER
22
n
22
SER
22
L
CYS
23
n
23
CYS
23
L
ARG
24
n
24
ARG
24
L
ALA
25
n
25
ALA
25
L
SER
26
n
26
SER
26
L
GLU
27
n
27
GLU
27
L
SER
27
n
28
A
SER
27
L
VAL
27
n
29
B
VAL
27
L
ASP
27
n
30
C
ASP
27
L
SER
27
n
31
D
SER
27
L
TYR
28
n
32
TYR
28
L
GLY
29
n
33
GLY
29
L
LYS
30
n
34
LYS
30
L
SER
31
n
35
SER
31
L
PHE
32
n
36
PHE
32
L
MET
33
n
37
MET
33
L
HIS
34
n
38
HIS
34
L
TRP
35
n
39
TRP
35
L
TYR
36
n
40
TYR
36
L
GLN
37
n
41
GLN
37
L
GLN
38
n
42
GLN
38
L
LYS
39
n
43
LYS
39
L
PRO
40
n
44
PRO
40
L
GLY
41
n
45
GLY
41
L
GLN
42
n
46
GLN
42
L
PRO
43
n
47
PRO
43
L
PRO
44
n
48
PRO
44
L
LYS
45
n
49
LYS
45
L
VAL
46
n
50
VAL
46
L
LEU
47
n
51
LEU
47
L
ILE
48
n
52
ILE
48
L
TYR
49
n
53
TYR
49
L
ILE
50
n
54
ILE
50
L
ALA
51
n
55
ALA
51
L
SER
52
n
56
SER
52
L
ASN
53
n
57
ASN
53
L
LEU
54
n
58
LEU
54
L
GLU
55
n
59
GLU
55
L
SER
56
n
60
SER
56
L
GLY
57
n
61
GLY
57
L
VAL
58
n
62
VAL
58
L
PRO
59
n
63
PRO
59
L
ALA
60
n
64
ALA
60
L
ARG
61
n
65
ARG
61
L
PHE
62
n
66
PHE
62
L
SER
63
n
67
SER
63
L
GLY
64
n
68
GLY
64
L
SER
65
n
69
SER
65
L
GLY
66
n
70
GLY
66
L
SER
67
n
71
SER
67
L
ARG
68
n
72
ARG
68
L
THR
69
n
73
THR
69
L
ASP
70
n
74
ASP
70
L
PHE
71
n
75
PHE
71
L
THR
72
n
76
THR
72
L
LEU
73
n
77
LEU
73
L
THR
74
n
78
THR
74
L
ILE
75
n
79
ILE
75
L
ASP
76
n
80
ASP
76
L
PRO
77
n
81
PRO
77
L
VAL
78
n
82
VAL
78
L
GLU
79
n
83
GLU
79
L
ALA
80
n
84
ALA
80
L
ASP
81
n
85
ASP
81
L
ASP
82
n
86
ASP
82
L
ALA
83
n
87
ALA
83
L
ALA
84
n
88
ALA
84
L
THR
85
n
89
THR
85
L
TYR
86
n
90
TYR
86
L
TYR
87
n
91
TYR
87
L
CYS
88
n
92
CYS
88
L
GLN
89
n
93
GLN
89
L
GLN
90
n
94
GLN
90
L
ASN
91
n
95
ASN
91
L
ASN
92
n
96
ASN
92
L
GLU
93
n
97
GLU
93
L
ASP
94
n
98
ASP
94
L
PRO
95
n
99
PRO
95
L
PRO
96
n
100
PRO
96
L
THR
97
n
101
THR
97
L
PHE
98
n
102
PHE
98
L
GLY
99
n
103
GLY
99
L
ALA
100
n
104
ALA
100
L
GLY
101
n
105
GLY
101
L
THR
102
n
106
THR
102
L
LYS
103
n
107
LYS
103
L
LEU
104
n
108
LEU
104
L
GLU
105
n
109
GLU
105
L
MET
106
n
110
MET
106
L
ARG
107
n
111
ARG
107
L
ARG
108
n
112
ARG
108
L
ALA
109
n
113
ALA
109
L
ASP
110
n
114
ASP
110
L
ALA
111
n
115
ALA
111
L
ALA
112
n
116
ALA
112
L
PRO
113
n
117
PRO
113
L
THR
114
n
118
THR
114
L
VAL
115
n
119
VAL
115
L
SER
116
n
120
SER
116
L
ILE
117
n
121
ILE
117
L
PHE
118
n
122
PHE
118
L
PRO
119
n
123
PRO
119
L
PRO
120
n
124
PRO
120
L
SER
121
n
125
SER
121
L
SER
122
n
126
SER
122
L
GLU
123
n
127
GLU
123
L
GLN
124
n
128
GLN
124
L
LEU
125
n
129
LEU
125
L
THR
126
n
130
THR
126
L
SER
127
n
131
SER
127
L
GLY
128
n
132
GLY
128
L
GLY
129
n
133
GLY
129
L
ALA
130
n
134
ALA
130
L
SER
131
n
135
SER
131
L
VAL
132
n
136
VAL
132
L
VAL
133
n
137
VAL
133
L
CYS
134
n
138
CYS
134
L
PHE
135
n
139
PHE
135
L
LEU
136
n
140
LEU
136
L
ASN
137
n
141
ASN
137
L
ASN
138
n
142
ASN
138
L
PHE
139
n
143
PHE
139
L
TYR
140
n
144
TYR
140
L
PRO
141
n
145
PRO
141
L
LYS
142
n
146
LYS
142
L
ASP
143
n
147
ASP
143
L
ILE
144
n
148
ILE
144
L
ASN
145
n
149
ASN
145
L
VAL
146
n
150
VAL
146
L
LYS
147
n
151
LYS
147
L
TRP
148
n
152
TRP
148
L
LYS
149
n
153
LYS
149
L
ILE
150
n
154
ILE
150
L
ASP
151
n
155
ASP
151
L
GLY
152
n
156
GLY
152
L
SER
153
n
157
SER
153
L
GLU
154
n
158
GLU
154
L
ARG
155
n
159
ARG
155
L
GLN
156
n
160
GLN
156
L
ASN
157
n
161
ASN
157
L
GLY
158
n
162
GLY
158
L
VAL
159
n
163
VAL
159
L
LEU
160
n
164
LEU
160
L
ASN
161
n
165
ASN
161
L
SER
162
n
166
SER
162
L
TRP
163
n
167
TRP
163
L
THR
164
n
168
THR
164
L
ASP
165
n
169
ASP
165
L
GLN
166
n
170
GLN
166
L
ASP
167
n
171
ASP
167
L
SER
168
n
172
SER
168
L
LYS
169
n
173
LYS
169
L
ASP
170
n
174
ASP
170
L
SER
171
n
175
SER
171
L
THR
172
n
176
THR
172
L
TYR
173
n
177
TYR
173
L
SER
174
n
178
SER
174
L
MET
175
n
179
MET
175
L
SER
176
n
180
SER
176
L
SER
177
n
181
SER
177
L
THR
178
n
182
THR
178
L
LEU
179
n
183
LEU
179
L
THR
180
n
184
THR
180
L
LEU
181
n
185
LEU
181
L
THR
182
n
186
THR
182
L
LYS
183
n
187
LYS
183
L
ASP
184
n
188
ASP
184
L
GLU
185
n
189
GLU
185
L
TYR
186
n
190
TYR
186
L
GLU
187
n
191
GLU
187
L
ARG
188
n
192
ARG
188
L
HIS
189
n
193
HIS
189
L
ASN
190
n
194
ASN
190
L
SER
191
n
195
SER
191
L
TYR
192
n
196
TYR
192
L
THR
193
n
197
THR
193
L
CYS
194
n
198
CYS
194
L
GLU
195
n
199
GLU
195
L
ALA
196
n
200
ALA
196
L
THR
197
n
201
THR
197
L
HIS
198
n
202
HIS
198
L
LYS
199
n
203
LYS
199
L
THR
200
n
204
THR
200
L
SER
201
n
205
SER
201
L
THR
202
n
206
THR
202
L
SER
203
n
207
SER
203
L
PRO
204
n
208
PRO
204
L
ILE
205
n
209
ILE
205
L
VAL
206
n
210
VAL
206
L
LYS
207
n
211
LYS
207
L
SER
208
n
212
SER
208
L
PHE
209
n
213
PHE
209
L
ASN
210
n
214
ASN
210
L
ARG
211
n
215
ARG
211
L
GLN
1
n
1
GLN
1
H
VAL
2
n
2
VAL
2
H
LYS
3
n
3
LYS
3
H
LEU
4
n
4
LEU
4
H
GLN
5
n
5
GLN
5
H
GLU
6
n
6
GLU
6
H
SER
7
n
7
SER
7
H
GLY
8
n
8
GLY
8
H
PRO
9
n
9
PRO
9
H
ALA
10
n
10
ALA
10
H
VAL
11
n
11
VAL
11
H
ILE
12
n
12
ILE
12
H
LYS
13
n
13
LYS
13
H
PRO
14
n
14
PRO
14
H
SER
15
n
15
SER
15
H
GLN
16
n
16
GLN
16
H
SER
17
n
17
SER
17
H
LEU
18
n
18
LEU
18
H
SER
19
n
19
SER
19
H
LEU
20
n
20
LEU
20
H
THR
21
n
21
THR
21
H
CYS
22
n
22
CYS
22
H
ILE
23
n
23
ILE
23
H
VAL
24
n
24
VAL
24
H
SER
25
n
25
SER
25
H
GLY
26
n
26
GLY
26
H
PHE
27
n
27
PHE
27
H
SER
28
n
28
SER
28
H
ILE
29
n
29
ILE
29
H
THR
30
n
30
THR
30
H
ARG
31
n
31
ARG
31
H
THR
32
n
32
THR
32
H
ASN
33
n
33
ASN
33
H
TYR
34
n
34
TYR
34
H
CYS
35
n
35
CYS
35
H
TRP
35
n
36
A
TRP
35
H
HIS
35
n
37
B
HIS
35
H
TRP
36
n
38
TRP
36
H
ILE
37
n
39
ILE
37
H
ARG
38
n
40
ARG
38
H
GLN
39
n
41
GLN
39
H
ALA
40
n
42
ALA
40
H
PRO
41
n
43
PRO
41
H
GLY
42
n
44
GLY
42
H
LYS
43
n
45
LYS
43
H
GLY
44
n
46
GLY
44
H
LEU
45
n
47
LEU
45
H
GLU
46
n
48
GLU
46
H
TRP
47
n
49
TRP
47
H
MET
48
n
50
MET
48
H
GLY
49
n
51
GLY
49
H
ARG
50
n
52
ARG
50
H
ILE
51
n
53
ILE
51
H
CYS
52
n
54
CYS
52
H
TYR
53
n
55
TYR
53
H
GLU
54
n
56
GLU
54
H
GLY
55
n
57
GLY
55
H
SER
56
n
58
SER
56
H
ILE
57
n
59
ILE
57
H
TYR
58
n
60
TYR
58
H
TYR
59
n
61
TYR
59
H
SER
60
n
62
SER
60
H
PRO
61
n
63
PRO
61
H
SER
62
n
64
SER
62
H
ILE
63
n
65
ILE
63
H
LYS
64
n
66
LYS
64
H
SER
65
n
67
SER
65
H
ARG
66
n
68
ARG
66
H
SER
67
n
69
SER
67
H
THR
68
n
70
THR
68
H
ILE
69
n
71
ILE
69
H
SER
70
n
72
SER
70
H
ARG
71
n
73
ARG
71
H
ASP
72
n
74
ASP
72
H
THR
73
n
75
THR
73
H
SER
74
n
76
SER
74
H
LEU
75
n
77
LEU
75
H
ASN
76
n
78
ASN
76
H
LYS
77
n
79
LYS
77
H
PHE
78
n
80
PHE
78
H
PHE
79
n
81
PHE
79
H
ILE
80
n
82
ILE
80
H
GLN
81
n
83
GLN
81
H
LEU
82
n
84
LEU
82
H
ILE
82
n
85
A
ILE
82
H
SER
82
n
86
B
SER
82
H
VAL
82
n
87
C
VAL
82
H
THR
83
n
88
THR
83
H
ASN
84
n
89
ASN
84
H
GLU
85
n
90
GLU
85
H
ASP
86
n
91
ASP
86
H
THR
87
n
92
THR
87
H
ALA
88
n
93
ALA
88
H
MET
89
n
94
MET
89
H
TYR
90
n
95
TYR
90
H
TYR
91
n
96
TYR
91
H
CYS
92
n
97
CYS
92
H
SER
93
n
98
SER
93
H
ARG
94
n
99
ARG
94
H
GLU
95
n
100
GLU
95
H
ASN
96
n
101
ASN
96
H
HIS
97
n
102
HIS
97
H
MET
98
n
103
MET
98
H
TYR
99
n
104
TYR
99
H
GLU
100
n
105
GLU
100
H
THR
100
n
106
A
THR
100
H
TYR
100
n
107
B
TYR
100
H
PHE
100
n
108
C
PHE
100
H
ASP
101
n
109
ASP
101
H
VAL
102
n
110
VAL
102
H
TRP
103
n
111
TRP
103
H
GLY
104
n
112
GLY
104
H
GLN
105
n
113
GLN
105
H
GLY
106
n
114
GLY
106
H
THR
107
n
115
THR
107
H
THR
108
n
116
THR
108
H
VAL
109
n
117
VAL
109
H
THR
110
n
118
THR
110
H
VAL
111
n
119
VAL
111
H
SER
112
n
120
SER
112
H
SER
113
n
121
SER
113
H
ALA
114
n
122
ALA
114
H
LYS
115
n
123
LYS
115
H
THR
116
n
124
THR
116
H
THR
117
n
125
THR
117
H
PRO
118
n
126
PRO
118
H
PRO
119
n
127
PRO
119
H
SER
120
n
128
SER
120
H
VAL
121
n
129
VAL
121
H
TYR
122
n
130
TYR
122
H
PRO
123
n
131
PRO
123
H
LEU
124
n
132
LEU
124
H
ALA
125
n
133
ALA
125
H
PRO
126
n
134
PRO
126
H
GLY
127
n
135
GLY
127
H
SER
128
n
136
SER
128
H
ALA
129
n
137
ALA
129
H
ALA
130
n
138
ALA
130
H
GLN
133
n
139
GLN
133
H
THR
134
n
140
THR
134
H
ASN
135
n
141
ASN
135
H
SER
136
n
142
SER
136
H
MET
137
n
143
MET
137
H
VAL
138
n
144
VAL
138
H
THR
139
n
145
THR
139
H
LEU
140
n
146
LEU
140
H
GLY
141
n
147
GLY
141
H
CYS
142
n
148
CYS
142
H
LEU
143
n
149
LEU
143
H
VAL
144
n
150
VAL
144
H
LYS
145
n
151
LYS
145
H
GLY
146
n
152
GLY
146
H
TYR
147
n
153
TYR
147
H
PHE
148
n
154
PHE
148
H
PRO
149
n
155
PRO
149
H
GLU
150
n
156
GLU
150
H
PRO
151
n
157
PRO
151
H
VAL
152
n
158
VAL
152
H
THR
153
n
159
THR
153
H
VAL
154
n
160
VAL
154
H
THR
156
n
161
THR
156
H
TRP
157
n
162
TRP
157
H
ASN
162
n
163
ASN
162
H
SER
163
n
164
SER
163
H
GLY
164
n
165
GLY
164
H
SER
165
n
166
SER
165
H
LEU
166
n
167
LEU
166
H
SER
167
n
168
SER
167
H
SER
168
n
169
SER
168
H
GLY
169
n
170
GLY
169
H
VAL
171
n
171
VAL
171
H
HIS
172
n
172
HIS
172
H
THR
173
n
173
THR
173
H
PHE
174
n
174
PHE
174
H
PRO
175
n
175
PRO
175
H
ALA
176
n
176
ALA
176
H
VAL
177
n
177
VAL
177
H
LEU
178
n
178
LEU
178
H
GLN
179
n
179
GLN
179
H
SER
180
n
180
SER
180
H
ASP
183
n
181
ASP
183
H
LEU
184
n
182
LEU
184
H
TYR
185
n
183
TYR
185
H
THR
186
n
184
THR
186
H
LEU
187
n
185
LEU
187
H
SER
188
n
186
SER
188
H
SER
189
n
187
SER
189
H
SER
190
n
188
SER
190
H
VAL
191
n
189
VAL
191
H
THR
192
n
190
THR
192
H
VAL
193
n
191
VAL
193
H
PRO
194
n
192
PRO
194
H
SER
195
n
193
SER
195
H
SER
196
n
194
SER
196
H
PRO
198
n
195
PRO
198
H
ARG
199
n
196
ARG
199
H
PRO
200
n
197
PRO
200
H
SER
202
n
198
SER
202
H
GLU
203
n
199
GLU
203
H
THR
204
n
200
THR
204
H
VAL
205
n
201
VAL
205
H
THR
206
n
202
THR
206
H
CYS
208
n
203
CYS
208
H
ASN
209
n
204
ASN
209
H
VAL
210
n
205
VAL
210
H
ALA
211
n
206
ALA
211
H
HIS
212
n
207
HIS
212
H
PRO
213
n
208
PRO
213
H
ALA
214
n
209
ALA
214
H
SER
215
n
210
SER
215
H
SER
216
n
211
SER
216
H
THR
217
n
212
THR
217
H
LYS
218
n
213
LYS
218
H
VAL
219
n
214
VAL
219
H
ASP
220
n
215
ASP
220
H
LYS
221
n
216
LYS
221
H
LYS
222
n
217
LYS
222
H
ILE
223
n
218
ILE
223
H
VAL
224
n
219
VAL
224
H
PRO
225
n
220
PRO
225
H
ARG
226
n
221
ARG
226
H
n
1
308
P
n
2
309
P
n
3
310
P
n
4
311
P
n
5
312
P
n
6
313
P
n
7
314
P
HIS
315
n
8
HIS
315
P
ILE
316
n
9
ILE
316
P
GLY
319
n
10
GLY
319
P
PRO
320
n
11
PRO
320
P
GLY
321
n
12
GLY
321
P
ARG
322
n
13
ARG
322
P
ALA
323
n
14
ALA
323
P
PHE
324
n
15
PHE
324
P
TYR
325
n
16
TYR
325
P
THR
326
n
17
THR
326
P
n
18
327
P
n
19
328
P
n
20
329
P
n
21
330
P
n
22
331
P
n
23
332
P
n
24
333
P
author_and_software_defined_assembly
PISA
3
trimeric
4520
-30
19390
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
L
O
SER
7
A
O
SER
7
L
N
SER
22
A
N
SER
22
L
N
CYS
23
A
N
CYS
23
L
O
PHE
71
A
O
PHE
75
L
O
THR
74
A
O
THR
78
L
N
SER
63
A
N
SER
67
L
N
LEU
11
A
N
LEU
11
L
O
LYS
103
A
O
LYS
107
L
N
LEU
104
A
N
LEU
108
L
O
ALA
84
A
O
ALA
88
L
O
GLN
89
A
O
GLN
93
L
N
HIS
34
A
N
HIS
38
L
O
GLN
37
A
O
GLN
41
L
N
LYS
45
A
N
LYS
49
L
N
TYR
49
A
N
TYR
53
L
O
ASN
53
A
O
ASN
57
L
N
LEU
11
A
N
LEU
11
L
O
LYS
103
A
O
LYS
107
L
N
LEU
104
A
N
LEU
108
L
O
ALA
84
A
O
ALA
88
L
N
GLN
90
A
N
GLN
94
L
O
THR
97
A
O
THR
101
L
O
PHE
118
A
O
PHE
122
L
N
VAL
133
A
N
VAL
137
L
O
PHE
139
A
O
PHE
143
L
N
TYR
173
A
N
TYR
177
L
N
THR
178
A
N
THR
182
L
O
LEU
160
A
O
LEU
164
L
N
LYS
149
A
N
LYS
153
L
O
THR
193
A
O
THR
197
L
O
HIS
198
A
O
HIS
202
L
N
SER
201
A
N
SER
205
H
O
SER
7
B
O
SER
7
H
N
THR
21
B
N
THR
21
H
N
CYS
22
B
N
CYS
22
H
O
PHE
78
B
O
PHE
80
H
N
GLN
81
B
N
GLN
83
H
O
THR
68
B
O
THR
70
H
N
TYR
58
B
N
TYR
60
H
O
ARG
50
B
O
ARG
52
H
N
GLN
39
B
N
GLN
41
H
O
MET
89
B
O
MET
94
H
N
TYR
58
B
N
TYR
60
H
O
ARG
50
B
O
ARG
52
H
N
GLN
39
B
N
GLN
41
H
O
MET
89
B
O
MET
94
H
N
TYR
90
B
N
TYR
95
H
O
THR
107
B
O
THR
115
H
O
THR
110
B
O
THR
118
H
N
ILE
12
B
N
ILE
12
H
N
LEU
124
B
N
LEU
132
H
O
GLY
141
B
O
GLY
147
H
O
TYR
147
B
O
TYR
153
H
N
TYR
185
B
N
TYR
183
H
N
SER
190
B
N
SER
188
H
O
HIS
172
B
O
HIS
172
H
N
THR
156
B
N
THR
161
H
O
ASN
209
B
O
ASN
204
H
N
HIS
212
B
N
HIS
207
H
O
THR
217
B
O
THR
212
1
P
TYR
308
C
TYR
1
1
Y
1
P
ASN
309
C
ASN
2
1
Y
1
P
LYS
310
C
LYS
3
1
Y
1
P
ARG
311
C
ARG
4
1
Y
1
P
LYS
312
C
LYS
5
1
Y
1
P
ARG
313
C
ARG
6
1
Y
1
P
ILE
314
C
ILE
7
1
Y
1
P
THR
327
C
THR
18
1
Y
1
P
LYS
328
C
LYS
19
1
Y
1
P
ASN
329
C
ASN
20
1
Y
1
P
ILE
330
C
ILE
21
1
Y
1
P
ILE
331
C
ILE
22
1
Y
1
P
GLY
332
C
GLY
23
1
Y
1
P
CYS
333
C
CYS
24
1
Y
1
H
ARG
199
10.37
1
L
ARG
211
0.134
SIDE CHAIN
1
15.72
2.30
115.30
131.02
L
L
L
CA
CB
CG
LEU
LEU
LEU
11
11
11
N
1
6.65
0.80
106.30
112.95
L
L
L
CD1
CG
CD2
TRP
TRP
TRP
35
35
35
N
1
-7.84
1.30
127.00
119.16
L
L
L
CB
CG
CD1
TRP
TRP
TRP
35
35
35
N
1
-5.47
0.80
107.30
101.83
L
L
L
CE2
CD2
CG
TRP
TRP
TRP
35
35
35
N
1
3.52
0.50
120.30
123.82
L
L
L
NE
CZ
NH1
ARG
ARG
ARG
61
61
61
N
1
13.64
2.20
113.40
127.04
L
L
L
CA
CB
CG
GLU
GLU
GLU
105
105
105
N
1
-11.05
1.80
110.60
99.55
L
L
L
N
CA
CB
MET
MET
MET
106
106
106
N
1
-22.72
3.00
112.40
89.68
L
L
L
CB
CG
SD
MET
MET
MET
106
106
106
N
1
-10.37
1.60
110.90
100.53
L
L
L
CG1
CB
CG2
VAL
VAL
VAL
133
133
133
N
1
6.91
0.80
106.30
113.21
L
L
L
CD1
CG
CD2
TRP
TRP
TRP
148
148
148
N
1
-6.21
0.80
107.30
101.09
L
L
L
CE2
CD2
CG
TRP
TRP
TRP
148
148
148
N
1
-15.13
2.20
117.20
102.07
L
L
L
CA
C
N
ARG
ARG
GLN
155
155
156
Y
1
6.98
0.80
106.30
113.28
L
L
L
CD1
CG
CD2
TRP
TRP
TRP
163
163
163
N
1
-6.17
0.80
107.30
101.13
L
L
L
CE2
CD2
CG
TRP
TRP
TRP
163
163
163
N
1
-4.00
0.60
121.00
117.00
L
L
L
CB
CG
CD2
TYR
TYR
TYR
186
186
186
N
1
5.99
0.50
120.30
126.29
L
L
L
NE
CZ
NH1
ARG
ARG
ARG
211
211
211
N
1
-9.06
0.50
120.30
111.24
L
L
L
NE
CZ
NH2
ARG
ARG
ARG
211
211
211
N
1
9.02
1.10
114.20
123.22
H
H
H
CA
CB
SG
CYS
CYS
CYS
35
35
35
N
A
A
A
1
5.72
0.80
106.30
112.02
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
35
35
35
N
B
B
B
1
-10.47
1.60
129.70
119.23
H
H
H
CB
CG
CD2
HIS
HIS
HIS
35
35
35
N
1
5.18
0.80
106.30
111.48
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
36
36
36
N
1
-5.34
0.80
107.30
101.96
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
36
36
36
N
1
6.14
0.50
120.30
126.44
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
38
38
38
N
1
-3.39
0.50
120.30
116.91
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
38
38
38
N
1
7.09
0.80
106.30
113.39
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
47
47
47
N
1
-5.81
0.80
107.30
101.49
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
47
47
47
N
1
-13.68
1.90
111.00
97.32
H
H
H
CA
CB
CG1
ILE
ILE
ILE
63
63
63
N
1
3.70
0.50
120.30
124.00
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
66
66
66
N
1
-3.13
0.50
120.30
117.17
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
66
66
66
N
1
3.40
0.50
120.30
123.70
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
71
71
71
N
A
A
A
1
8.86
1.40
112.40
121.26
H
H
H
CA
CB
CG2
THR
THR
THR
100
100
100
N
1
5.33
0.80
106.30
111.63
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
103
103
103
N
1
-5.19
0.80
107.30
102.11
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
103
103
103
N
1
-4.25
0.60
121.00
116.75
H
H
H
CB
CG
CD2
TYR
TYR
TYR
147
147
147
N
1
-8.32
1.30
127.00
118.68
H
H
H
CB
CG
CD1
TRP
TRP
TRP
157
157
157
N
1
-10.47
1.40
111.70
101.23
H
H
H
CA
N
CD
PRO
PRO
PRO
175
175
175
N
1
-12.00
1.90
111.40
99.40
H
H
H
CB
CA
C
VAL
VAL
VAL
191
191
191
N
1
9.73
1.50
119.30
129.03
H
H
H
C
N
CA
SER
PRO
PRO
196
198
198
Y
1
-15.68
2.10
128.40
112.72
H
H
H
C
N
CD
SER
PRO
PRO
196
198
198
Y
1
3.26
0.50
120.30
123.56
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
199
199
199
N
1
-4.20
0.50
120.30
116.10
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
199
199
199
N
1
-16.81
2.70
111.00
94.19
H
H
H
N
CA
C
ARG
ARG
ARG
199
199
199
N
1
L
L
NE2
CD2
HIS
HIS
34
34
-0.079
0.011
1.373
1.294
N
1
L
L
NE2
CD2
HIS
HIS
189
189
-0.074
0.011
1.373
1.299
N
B
B
1
H
H
NE2
CD2
HIS
HIS
35
35
-0.091
0.011
1.373
1.282
N
1
H
H
CG
CD2
TRP
TRP
47
47
-0.102
0.017
1.432
1.330
N
1
H
H
NE2
CD2
HIS
HIS
97
97
-0.067
0.011
1.373
1.306
N
1
H
H
NE2
CD2
HIS
HIS
172
172
-0.069
0.011
1.373
1.304
N
1
H
H
NE2
CD2
HIS
HIS
212
212
-0.067
0.011
1.373
1.306
N
1
L
ILE
2
-28.74
126.90
1
L
PHE
32
-91.52
57.28
1
L
ILE
50
29.24
59.73
1
L
ALA
51
64.72
-40.74
1
L
ALA
60
-39.32
-32.69
1
L
ARG
68
63.55
-74.05
1
L
ASP
76
-161.24
119.56
1
L
ALA
80
-22.93
-59.89
1
L
ALA
83
-60.55
98.04
1
L
ASN
91
-156.96
51.85
1
L
SER
127
-79.93
27.44
1
L
ASP
151
-26.23
84.62
1
L
GLN
156
-24.49
-48.94
1
L
THR
164
-59.99
174.89
1
L
LYS
169
-134.37
-46.62
1
H
SER
15
62.76
65.84
1
H
PHE
27
-177.93
147.10
1
H
ASN
33
87.11
-23.38
1
H
TYR
53
-23.87
-43.51
1
H
GLU
54
-90.91
33.45
1
H
SER
62
110.70
-51.84
1
H
ARG
66
-148.17
39.22
B
1
H
SER
82
34.96
68.65
1
H
GLU
100
-143.88
-33.56
1
H
SER
128
32.29
52.92
1
H
ASN
135
59.62
-139.34
1
H
SER
180
47.25
86.01
1
H
SER
196
-143.63
-48.31
1
P
ARG
322
-19.22
-49.54
1
P
PHE
324
-108.62
40.86
0.21
0.21
3.0
12.0
15181
1
0.0
3.0
12.0
0
3442
0
0
3442
0.018
3.8
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
IGG1 FAB FRAGMENT (59.1) COMPLEXED WITH HIV-1 GP120 (MN ISOLATE) FRAGMENT (RESIDUES 308 - 332)
CRYSTAL STRUCTURE OF THE PRINCIPAL NEUTRALIZING SITE OF HIV-1
1
N
N
2
N
N
3
N
N
L
GLU
79
A
GLU
83
HELX_P
L
ALA
83
A
ALA
87
5
1
5
L
SER
121
A
SER
125
HELX_P
L
SER
127
A
SER
131
1
2
7
L
LYS
183
A
LYS
187
HELX_P
L
ARG
188
A
ARG
192
1
3
6
H
ILE
63
B
ILE
65
HELX_P
H
SER
65
B
SER
67
5
4
3
H
THR
83
B
THR
88
HELX_P
H
THR
87
B
THR
92
5
5
5
H
SER
163
B
SER
164
HELX_P
H
SER
165
B
SER
166
5
6
3
H
PRO
213
B
PRO
208
HELX_P
H
SER
216
B
SER
211
5
7
4
P
GLY
321
C
GLY
12
HELX_P
P
TYR
325
C
TYR
16
5
8
5
disulf
2.035
L
CYS
23
A
SG
CYS
23
1_555
L
CYS
88
A
SG
CYS
92
1_555
disulf
2.013
L
CYS
134
A
SG
CYS
138
1_555
L
CYS
194
A
SG
CYS
198
1_555
disulf
2.029
H
CYS
22
B
SG
CYS
22
1_555
H
CYS
92
B
SG
CYS
97
1_555
disulf
2.033
H
CYS
35
B
SG
CYS
35
1_555
H
CYS
52
B
SG
CYS
54
1_555
disulf
1.982
H
CYS
142
B
SG
CYS
148
1_555
H
CYS
208
B
SG
CYS
203
1_555
COMPLEX(ANTIBODY/HIV-1 FRAGMENT)
COMPLEX(ANTIBODY-HIV-1 FRAGMENT), COMPLEX(ANTIBODY-HIV-1 FRAGMENT) complex
L
SER
7
A
SER
7
1
L
PRO
8
A
PRO
8
-1.59
L
ASP
76
A
ASP
80
1
L
PRO
77
A
PRO
81
-0.25
L
ASP
94
A
ASP
98
1
L
PRO
95
A
PRO
99
-2.57
L
TYR
140
A
TYR
144
1
L
PRO
141
A
PRO
145
-1.38
H
PHE
148
B
PHE
154
1
H
PRO
149
B
PRO
155
-1.03
H
GLU
150
B
GLU
156
1
H
PRO
151
B
PRO
157
-0.81
H
ARG
199
B
ARG
196
1
H
PRO
200
B
PRO
197
-4.50
IGH1M_MOUSE
UNP
2
1
P01869
ENV_HV1MN
UNP
3
306
P05877
1ACY
PDB
1
1ACY
1
100
1ACY
114
226
P01869
H
1
122
221
306
328
1ACY
308
332
P05877
P
2
1
23
1
211
1ACY
1
211
1ACY
L
3
1
215
4
6
4
2
4
3
4
5
6
4
3
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
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
L
MET
4
A
MET
4
L
SER
7
A
SER
7
L
ALA
19
A
ALA
19
L
ALA
25
A
ALA
25
L
ASP
70
A
ASP
74
L
ILE
75
A
ILE
79
L
PHE
62
A
PHE
66
L
SER
67
A
SER
71
L
SER
10
A
SER
10
L
SER
14
A
SER
14
L
THR
102
A
THR
106
L
ARG
107
A
ARG
111
L
ALA
84
A
ALA
88
L
GLN
90
A
GLN
94
L
MET
33
A
MET
37
L
GLN
38
A
GLN
42
L
LYS
45
A
LYS
49
L
TYR
49
A
TYR
53
L
ASN
53
A
ASN
57
L
LEU
54
A
LEU
58
L
SER
10
A
SER
10
L
SER
14
A
SER
14
L
THR
102
A
THR
106
L
ARG
107
A
ARG
111
L
ALA
84
A
ALA
88
L
GLN
90
A
GLN
94
L
THR
97
A
THR
101
L
PHE
98
A
PHE
102
L
LYS
30
A
LYS
34
L
SER
31
A
SER
35
L
THR
114
A
THR
118
L
PHE
118
A
PHE
122
L
GLY
129
A
GLY
133
L
PHE
139
A
PHE
143
L
TYR
173
A
TYR
177
L
THR
182
A
THR
186
L
VAL
159
A
VAL
163
L
TRP
163
A
TRP
167
L
ASN
145
A
ASN
149
L
ILE
150
A
ILE
154
L
SER
191
A
SER
195
L
HIS
198
A
HIS
202
L
SER
201
A
SER
205
L
ASN
210
A
ASN
214
H
LYS
3
B
LYS
3
H
SER
7
B
SER
7
H
LEU
18
B
LEU
18
H
SER
25
B
SER
25
H
LYS
77
B
LYS
79
H
LEU
82
B
LEU
84
H
SER
67
B
SER
69
H
ARG
71
B
ARG
73
H
ILE
57
B
ILE
59
H
TYR
59
B
TYR
61
H
LEU
45
B
LEU
47
H
CYS
52
B
CYS
54
H
TYR
34
B
TYR
34
H
GLN
39
B
GLN
41
H
ALA
88
B
ALA
93
H
ASN
96
B
ASN
101
H
ILE
57
B
ILE
59
H
TYR
59
B
TYR
61
H
LEU
45
B
LEU
47
H
CYS
52
B
CYS
54
H
TYR
34
B
TYR
34
H
GLN
39
B
GLN
41
H
ALA
88
B
ALA
93
H
ASN
96
B
ASN
101
H
THR
107
B
THR
115
H
VAL
111
B
VAL
119
H
VAL
11
B
VAL
11
H
ILE
12
B
ILE
12
H
SER
120
B
SER
128
H
LEU
124
B
LEU
132
H
MET
137
B
MET
143
H
TYR
147
B
TYR
153
H
TYR
185
B
TYR
183
H
PRO
194
B
PRO
192
H
HIS
172
B
HIS
172
H
LEU
178
B
LEU
178
H
THR
153
B
THR
159
H
TRP
157
B
TRP
162
H
THR
206
B
THR
202
H
HIS
212
B
HIS
207
H
THR
217
B
THR
212
H
LYS
222
B
LYS
217
20
C 2 2 21