1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Tugarinov, V.
Zvi, A.
Levy, R.
Anglister, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
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
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
C
N
48
N
O
N
49
N
N
N
50
N
O
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
H
N
59
N
H
N
60
N
H
N
61
N
N
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
N
N
72
S
C
N
73
N
C
N
74
N
O
N
75
S
C
N
76
N
C
N
77
N
C
N
78
N
C
N
79
N
O
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
N
N
94
S
C
N
95
N
C
N
96
N
O
N
97
N
C
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
N
N
102
N
O
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
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
N
N
119
S
C
N
120
N
C
N
121
N
O
N
122
N
C
Y
123
N
C
Y
124
N
C
Y
125
N
C
Y
126
N
C
Y
127
N
C
Y
128
N
C
N
129
N
O
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
N
N
142
S
C
N
143
N
C
N
144
N
O
N
145
N
C
N
146
N
C
N
147
N
C
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
N
N
159
S
C
N
160
N
C
N
161
N
O
N
162
N
C
N
163
N
O
N
164
N
O
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
N
N
173
S
C
N
174
N
C
N
175
N
O
N
176
R
C
N
177
N
O
N
178
N
C
N
179
N
O
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
N
N
190
S
C
N
191
N
C
N
192
N
O
N
193
N
C
N
194
N
C
N
195
N
C
N
196
N
O
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
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
sing
N
51
N
sing
N
52
N
sing
N
53
N
doub
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
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
sing
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
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
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
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
doub
N
95
N
sing
N
96
N
sing
N
97
N
sing
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
sing
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
sing
N
117
N
sing
N
118
N
doub
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
Y
123
N
doub
Y
124
N
sing
Y
125
N
sing
N
126
N
sing
Y
127
N
doub
N
128
N
sing
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
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
doub
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
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
doub
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
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
6
331
335
10.1038/7567
10201400
A cis proline turn linking two beta-hairpin strands in the solution structure of an antibody-bound HIV-1IIIB V3 peptide.
1999
US
Biochemistry
BICHAW
0033
0006-2960
36
8619
8627
Conformation of the Principal Neutralizing Determinant of Human Immunodeficiency Virus Type 1 in Complex with an Anti-GP120 Virus Neutralizing Antibody Studied by Two-dimensional Nuclear Magnetic Resonance Difference Spectroscopy.
1997
10.2210/pdb1b03/pdb
pdb_00001b03
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
P1053 PEPTIDE REPRESENTS THE FULL ANTIBODY RECOGNIZED EPITOPE OF THE HIV-1IIIB GP120 V3 LOOP.
2017.406
PROTEIN (P1053 PEPTIDE)
1
syn
polymer
no
no
RKSIRIQRGPGRAFVTIG
RKSIRIQRGPGRAFVTIG
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conf
chem_comp_atom
chem_comp_bond
database_2
pdbx_nmr_software
repository
Initial release
Version format compliance
Version format compliance
Derived calculations
Data collection
Database references
1
0
1998-11-25
1
1
2008-04-26
1
2
2011-07-13
1
3
2017-11-29
1
4
2023-12-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
Y
RCSB
1998-11-17
REL
REL
THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
sample
THE STRUCTURE WAS DETERMINED IN COMPLEX WITH THE FV ANTIBODY FRAGMENT USING
ISOTOPE-FILTERED AND ISOTOPE-EDITED NMR WITH EITHER THE FV OR THE PEPTIDE
LABELLED WITH 15N AND 13C.
LEAST RESTRAINT VIOLATIONS
35
15N
13C FILTERED NOESY
7.1
305
K
AFTER INITIAL SIMULATED ANNEALING CALCULATIONS THE STRUCTURES WERE MINIMIZED
USING A FULL L-J POTENTIAL REPRESENTATION. THE CIS PEPTIDE BOND BETWEEN GLY 12
AND PRO 13 WAS PATHED CIS IN THE PROCESS OF STRUCTURE GENERATION.
HYBRID DG-SA
BRUNGER
refinement
X-PLOR
3.1
structure solution
NMRPipe
600
Bruker
DMX600
ARG
4
n
1
ARG
4
A
LYS
5
n
2
LYS
5
A
SER
6
n
3
SER
6
A
ILE
7
n
4
ILE
7
A
ARG
8
n
5
ARG
8
A
ILE
9
n
6
ILE
9
A
GLN
10
n
7
GLN
10
A
ARG
11
n
8
ARG
11
A
GLY
12
n
9
GLY
12
A
PRO
13
n
10
PRO
13
A
GLY
14
n
11
GLY
14
A
ARG
15
n
12
ARG
15
A
ALA
16
n
13
ALA
16
A
PHE
17
n
14
PHE
17
A
VAL
18
n
15
VAL
18
A
THR
19
n
16
THR
19
A
ILE
20
n
17
ILE
20
A
GLY
21
n
18
GLY
21
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
LYS
5
A
O
LYS
2
A
N
ILE
20
A
N
ILE
17
2
A
ALA
16
-169.52
-166.47
4
A
ARG
15
-62.28
88.22
5
A
ALA
16
-170.28
-168.12
6
A
ALA
16
-160.48
-165.16
8
A
ALA
16
-160.96
-169.32
10
A
ALA
16
-168.85
-166.63
14
A
ALA
16
-170.42
-168.13
19
A
ALA
16
-163.29
-168.86
21
A
ALA
16
-170.22
-174.74
23
A
ALA
16
-168.31
-164.61
35
A
ARG
15
-61.58
98.84
SOLUTION STRUCTURE OF THE ANTIBODY-BOUND HIV-1IIIB V3 PEPTIDE
1
N
N
VIRAL PROTEIN
P1053 STRUCTURE, Viral protein
A
GLY
12
A
GLY
9
1
A
PRO
13
A
PRO
10
0.07
A
GLY
12
A
GLY
9
2
A
PRO
13
A
PRO
10
0.14
A
GLY
12
A
GLY
9
3
A
PRO
13
A
PRO
10
0.04
A
GLY
12
A
GLY
9
4
A
PRO
13
A
PRO
10
0.01
A
GLY
12
A
GLY
9
5
A
PRO
13
A
PRO
10
0.18
A
GLY
12
A
GLY
9
6
A
PRO
13
A
PRO
10
0.13
A
GLY
12
A
GLY
9
7
A
PRO
13
A
PRO
10
0.12
A
GLY
12
A
GLY
9
8
A
PRO
13
A
PRO
10
0.13
A
GLY
12
A
GLY
9
9
A
PRO
13
A
PRO
10
-0.15
A
GLY
12
A
GLY
9
10
A
PRO
13
A
PRO
10
-0.07
A
GLY
12
A
GLY
9
11
A
PRO
13
A
PRO
10
0.06
A
GLY
12
A
GLY
9
12
A
PRO
13
A
PRO
10
-0.05
A
GLY
12
A
GLY
9
13
A
PRO
13
A
PRO
10
-0.03
A
GLY
12
A
GLY
9
14
A
PRO
13
A
PRO
10
0.11
A
GLY
12
A
GLY
9
15
A
PRO
13
A
PRO
10
0.00
A
GLY
12
A
GLY
9
16
A
PRO
13
A
PRO
10
-0.11
A
GLY
12
A
GLY
9
17
A
PRO
13
A
PRO
10
-0.02
A
GLY
12
A
GLY
9
18
A
PRO
13
A
PRO
10
0.24
A
GLY
12
A
GLY
9
19
A
PRO
13
A
PRO
10
0.16
A
GLY
12
A
GLY
9
20
A
PRO
13
A
PRO
10
-0.02
A
GLY
12
A
GLY
9
21
A
PRO
13
A
PRO
10
0.13
A
GLY
12
A
GLY
9
22
A
PRO
13
A
PRO
10
0.17
A
GLY
12
A
GLY
9
23
A
PRO
13
A
PRO
10
0.00
A
GLY
12
A
GLY
9
24
A
PRO
13
A
PRO
10
0.02
A
GLY
12
A
GLY
9
25
A
PRO
13
A
PRO
10
0.03
A
GLY
12
A
GLY
9
26
A
PRO
13
A
PRO
10
0.08
A
GLY
12
A
GLY
9
27
A
PRO
13
A
PRO
10
0.35
A
GLY
12
A
GLY
9
28
A
PRO
13
A
PRO
10
0.24
A
GLY
12
A
GLY
9
29
A
PRO
13
A
PRO
10
-0.17
A
GLY
12
A
GLY
9
30
A
PRO
13
A
PRO
10
0.04
A
GLY
12
A
GLY
9
31
A
PRO
13
A
PRO
10
-0.07
A
GLY
12
A
GLY
9
32
A
PRO
13
A
PRO
10
-0.12
A
GLY
12
A
GLY
9
33
A
PRO
13
A
PRO
10
0.05
A
GLY
12
A
GLY
9
34
A
PRO
13
A
PRO
10
-0.02
A
GLY
12
A
GLY
9
35
A
PRO
13
A
PRO
10
0.31
Q79428_9HIV1
UNP
1
Q79428
108
125
1B03
4
21
Q79428
A
1
1
18
2
anti-parallel
A
LYS
5
A
LYS
2
A
ILE
9
A
ILE
6
A
ALA
16
A
ALA
13
A
ILE
20
A
ILE
17
1
P 1