1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Phan Chan Du, A.
Limal, D.
Semetey, V.
Dali, H.
Jolivet, M.
Desgranges, C.
Cung, M.T.
Briand, J.P.
Petit, M.C.
Muller, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90
90
90
1
1
1
C2 H4 O
44.053
ACETYL GROUP
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C4 H9 N O3
119.119
(3R)-3-AMINO-4-HYDROXYBUTANOIC ACID
D-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
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 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
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
N
1
N
C
N
2
N
O
N
3
N
C
N
4
N
H
N
5
N
H
N
6
N
H
N
7
N
H
N
8
N
N
N
9
S
C
N
10
N
C
N
11
N
O
N
12
N
C
N
13
N
O
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
N
N
22
N
O
N
23
N
C
N
24
R
C
N
25
N
C
N
26
N
C
N
27
N
O
N
28
N
O
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
N
N
39
R
C
N
40
N
C
N
41
N
O
N
42
N
C
N
43
N
S
N
44
N
O
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
H
N
52
N
N
N
53
N
C
N
54
N
C
N
55
N
O
N
56
N
O
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
N
N
63
S
C
N
64
N
C
N
65
N
O
N
66
S
C
N
67
N
C
N
68
N
C
N
69
N
C
N
70
N
O
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
N
N
85
S
C
N
86
N
C
N
87
N
O
N
88
N
C
N
89
N
C
N
90
N
C
N
91
N
C
N
92
N
O
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
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
N
N
107
S
C
N
108
N
C
N
109
N
O
N
110
N
C
N
111
N
C
N
112
N
C
N
113
N
C
N
114
N
N
N
115
N
O
N
116
N
H
N
117
N
H
N
118
N
H
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
H
N
129
N
H
N
130
N
H
N
131
N
N
N
132
S
C
N
133
N
C
N
134
N
O
N
135
N
C
N
136
N
O
N
137
N
O
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
N
N
146
S
C
N
147
N
C
N
148
N
O
N
149
R
C
N
150
N
O
N
151
N
C
N
152
N
O
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
H
N
160
N
H
N
161
N
H
N
162
N
N
N
163
S
C
N
164
N
C
N
165
N
O
N
166
N
C
Y
167
N
C
Y
168
N
C
Y
169
N
C
Y
170
N
N
Y
171
N
C
Y
172
N
C
Y
173
N
C
Y
174
N
C
Y
175
N
C
N
176
N
O
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
1
N
doub
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
doub
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
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
doub
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
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
sing
N
54
N
doub
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
doub
N
64
N
sing
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
sing
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
doub
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
sing
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
doub
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
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
sing
N
127
N
sing
N
128
N
sing
N
129
N
doub
N
130
N
sing
N
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
sing
N
142
N
doub
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
Y
163
N
doub
Y
164
N
sing
Y
165
N
sing
N
166
N
sing
Y
167
N
doub
Y
168
N
sing
Y
169
N
sing
N
170
N
sing
Y
171
N
sing
Y
172
N
doub
N
173
N
sing
Y
174
N
doub
N
175
N
sing
Y
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
323
503
521
10.1016/S0022-2836(02)00701-5
12381305
Structural and immunological characterisation of heteroclitic peptide analogues corresponding to the 600-612 region of the HIV envelope gp41 glycoprotein.
2002
10.2210/pdb1j8n/pdb
pdb_00001j8n
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
SINGLE WAVELENGTH
M
x-ray
1
1.0
1393.694
HIV1 GP41 HSER analogue peptide Ace-Ile-Trp-Gly-Cys-beta3Ser-Gly-Lys-Leu-Ile-Cys-Thr-Thr-Ala
1
syn
polymer
no
yes
(ACE)IWGC(B3S)GKLICTTA
XIWGCSGKLICTTA
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
pdbx_nmr_software
pdbx_nmr_spectrometer
struct_conn
struct_ref_seq_dif
database_2
struct_ref_seq_dif
struct_site
atom_site
chem_comp_atom
chem_comp_bond
pdbx_validate_main_chain_plane
pdbx_validate_peptide_omega
pdbx_validate_rmsd_angle
pdbx_validate_torsion
repository
Initial release
Version format compliance
Version format compliance
Other
Data collection
Database references
Derived calculations
Database references
Derived calculations
Atomic model
Data collection
1
0
2003-07-01
1
1
2008-04-27
1
2
2011-07-13
1
3
2011-10-05
1
4
2020-06-24
1
5
2021-10-27
2
0
2023-11-15
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_ref_seq_dif.details
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_atom_site.auth_atom_id
_atom_site.label_atom_id
1IM7 entry contains the parent peptide coordinates.
RCSB
Y
RCSB
2001-05-22
REL
REL
THE PARENT SEQUENCE IWGCSGKLICTTA OCCURS IN HIV GP41 PROTEIN. This analogue contains a modified residue BSE which is a beta3-Ser (i.e. with an additional CH2 between NH and Calpha).
sample
THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES. NOESY EXPERIMENTS WITH MIXING TIMES FROM 80MS TO 800MS WERE RECORDED IN ORDER TO DEFINE THE BEST CONDITIONS IN ORDER TO AVOID SPIN DIFFUSION.
target function
50
27
2D NOESY
DQF-COSY
2D NOESY
ambient
298
K
50 INITIAL RANDOM STRUCTURES WERE CALCULATED USING SIMULATED ANNEALING IN DYANA SOFTWARE. REFINEMENT WAS DONE WITH 500 STEPS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K FOR EQUILIBRATION, 200PS MD UNDER NMR RESTRAINTS, AND 750PS CONJUGATED GRADIENT EM USING DISCOVER MODULE OF MSI SOFTWARE.
torsion angle dynamics , molecular dynamics, energy minimization
1
lowest energy
2mM peptide ; 500ul DMSO-D6
DMSO-D6
4mM peptide ; 500ul DMSO-D6
DMSO-D6
Bruker GMBH
collection
XwinNMR
2.6
Bartels C., Xia T., Billeter M., Guentert P. and Wuethrich K., (1995)J. Biomolecular NMR 5, 1-10
data analysis
XEASY
1.2
Guentert P., Mumenthaler C., Wuethrich K.
refinement
DYANA
1.5
Molecular Simulation Inc., San Diego
refinement
Discover
3
400
Bruker
AVANCE
600
Bruker
AVANCE
ACE
1
n
1
ACE
1
A
ILE
2
n
2
ILE
2
A
TRP
3
n
3
TRP
3
A
GLY
4
n
4
GLY
4
A
CYS
5
n
5
CYS
5
A
BSE
6
n
6
B3S
6
A
GLY
7
n
7
GLY
7
A
LYS
8
n
8
LYS
8
A
LEU
9
n
9
LEU
9
A
ILE
10
n
10
ILE
10
A
CYS
11
n
11
CYS
11
A
THR
12
n
12
THR
12
A
THR
13
n
13
THR
13
A
ALA
14
n
14
ALA
14
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
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
18
A
A
O
H
GLY
LEU
7
9
1.60
23
A
A
O
H
B3S
LYS
6
8
1.59
1
A
B3S
6
-16.02
4
A
B3S
6
-15.32
6
A
B3S
6
-16.10
7
A
B3S
6
10.74
8
A
B3S
6
-13.62
9
A
B3S
6
-13.41
10
A
B3S
6
10.13
11
A
B3S
6
-13.68
12
A
B3S
6
11.36
13
A
B3S
6
10.05
14
A
B3S
6
-15.57
15
A
B3S
6
12.50
16
A
B3S
6
-11.36
17
A
B3S
6
10.63
18
A
B3S
6
10.95
19
A
B3S
6
13.42
20
A
B3S
6
13.17
21
A
B3S
6
11.78
22
A
B3S
6
-16.93
24
A
B3S
6
-15.96
25
A
B3S
6
10.41
26
A
B3S
6
-10.99
27
A
B3S
6
-15.29
1
A
A
B3S
GLY
6
7
144.55
4
A
A
B3S
GLY
6
7
145.68
6
A
A
B3S
GLY
6
7
144.37
8
A
A
B3S
GLY
6
7
149.10
9
A
A
B3S
GLY
6
7
149.54
11
A
A
B3S
GLY
6
7
148.97
14
A
A
B3S
GLY
6
7
145.32
19
A
A
B3S
GLY
6
7
-149.73
22
A
A
B3S
GLY
6
7
143.26
24
A
A
B3S
GLY
6
7
144.59
27
A
A
B3S
GLY
6
7
145.74
2
-22.68
2.00
116.20
93.52
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
3
-27.35
2.00
116.20
88.85
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
5
-23.98
2.00
116.20
92.22
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
7
-20.77
2.00
116.20
95.43
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
8
-14.74
2.00
116.20
101.46
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
9
-15.37
2.00
116.20
100.83
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
10
-22.22
2.00
116.20
93.98
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
11
-14.43
2.00
116.20
101.77
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
12
-19.34
2.00
116.20
96.86
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
13
-22.37
2.00
116.20
93.83
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
15
-16.36
2.00
116.20
99.84
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
16
-20.88
2.00
116.20
95.32
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
17
-21.16
2.00
116.20
95.04
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
18
-20.50
2.00
116.20
95.70
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
19
-13.37
2.00
116.20
102.83
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
20
-14.07
2.00
116.20
102.13
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
21
-18.41
2.00
116.20
97.79
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
23
-29.05
2.00
116.20
87.15
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
25
-21.56
2.00
116.20
94.64
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
26
-21.68
2.00
116.20
94.52
A
A
A
CA
C
N
B3S
B3S
GLY
6
6
7
Y
1
A
B3S
6
-114.89
-3.42
1
A
LYS
8
-90.16
41.23
1
A
LEU
9
-107.17
-65.56
1
A
ILE
10
-151.41
81.47
1
A
THR
13
-165.06
89.27
2
A
B3S
6
-101.74
-22.54
2
A
LEU
9
-165.29
-43.02
2
A
THR
12
-163.75
116.35
2
A
THR
13
-165.13
101.07
3
A
LEU
9
-165.02
-43.57
3
A
THR
13
-162.73
-81.66
4
A
B3S
6
-106.95
-5.80
4
A
LYS
8
-68.70
66.68
4
A
LEU
9
-165.05
-43.51
4
A
THR
13
-157.45
-78.22
5
A
B3S
6
-86.15
33.15
5
A
LYS
8
-69.00
66.60
5
A
LEU
9
-153.60
-46.30
5
A
THR
13
-165.11
107.66
6
A
B3S
6
-122.41
-3.40
6
A
LYS
8
-90.57
40.23
6
A
LEU
9
-108.44
-68.15
6
A
ILE
10
-166.06
110.31
6
A
THR
13
-162.14
-79.86
7
A
B3S
6
-104.84
-10.50
7
A
LEU
9
-165.37
-43.04
7
A
THR
13
-162.42
-83.19
8
A
B3S
6
-120.01
33.89
8
A
LYS
8
-69.10
63.82
8
A
LEU
9
-132.75
-45.07
8
A
ILE
10
-165.12
114.18
8
A
THR
13
-165.13
110.65
9
A
B3S
6
-111.56
14.40
9
A
LEU
9
-130.78
-45.18
9
A
ILE
10
-165.21
113.80
10
A
B3S
6
-104.11
-21.76
10
A
LEU
9
-165.54
-42.33
10
A
ILE
10
-162.95
112.76
10
A
THR
13
-165.15
106.55
11
A
B3S
6
-119.04
34.79
11
A
LYS
8
-68.66
66.26
11
A
LEU
9
-136.13
-45.34
11
A
ILE
10
-165.08
114.25
11
A
THR
13
-157.41
-78.21
12
A
TRP
3
-160.08
96.82
12
A
B3S
6
-112.03
-2.19
12
A
LEU
9
-165.75
-42.50
12
A
ILE
10
-165.05
114.92
12
A
THR
13
-161.94
-85.78
13
A
B3S
6
-156.51
57.24
13
A
LYS
8
-95.90
51.84
13
A
LEU
9
-166.12
-42.86
13
A
ILE
10
-165.63
112.94
13
A
THR
13
-162.32
106.29
14
A
B3S
6
-138.43
-13.60
14
A
LEU
9
-167.16
-72.33
14
A
THR
13
-162.44
-84.61
15
A
B3S
6
-64.34
86.07
15
A
LEU
9
-150.98
-68.49
15
A
ILE
10
-151.21
87.95
15
A
THR
13
-165.11
109.55
16
A
TRP
3
-95.08
36.97
16
A
B3S
6
-125.62
37.18
16
A
LEU
9
-165.74
-50.84
16
A
CYS
11
-86.08
48.33
16
A
THR
13
-157.38
-78.23
17
A
TRP
3
-162.51
37.43
17
A
CYS
5
-40.59
104.25
17
A
B3S
6
-105.96
1.23
17
A
LEU
9
-153.93
-45.44
17
A
THR
13
-163.44
94.92
18
A
B3S
6
-108.30
-13.73
18
A
LEU
9
-165.86
-51.64
18
A
CYS
11
-87.91
47.17
18
A
THR
13
-161.31
79.64
19
A
B3S
6
-80.52
103.91
19
A
LEU
9
-165.40
-42.67
19
A
CYS
11
-94.02
30.69
19
A
THR
13
-165.07
88.49
20
A
B3S
6
-71.54
95.62
20
A
LYS
8
-80.59
48.07
20
A
LEU
9
-138.13
-55.40
20
A
ILE
10
-153.02
81.02
20
A
THR
13
-162.03
98.23
21
A
B3S
6
-56.67
92.05
21
A
LEU
9
-153.57
-71.21
21
A
ILE
10
-151.74
84.95
21
A
THR
13
-164.73
108.70
22
A
B3S
6
-42.50
-7.52
22
A
THR
13
-165.09
95.53
23
A
B3S
6
-108.11
-58.10
23
A
LEU
9
-165.06
-43.33
23
A
THR
13
-157.41
-78.23
24
A
TRP
3
-144.48
38.21
24
A
B3S
6
-103.86
-4.86
24
A
LYS
8
-90.14
39.89
24
A
ILE
10
-167.06
115.58
24
A
THR
13
-163.73
108.62
25
A
B3S
6
-109.33
-22.37
25
A
LYS
8
-68.82
66.54
25
A
LEU
9
-165.45
-40.85
25
A
ILE
10
-166.83
116.67
25
A
THR
13
-162.14
-79.50
26
A
B3S
6
-110.10
-58.02
26
A
LEU
9
-166.54
-68.27
26
A
ILE
10
-165.78
112.93
26
A
THR
13
-165.16
109.59
27
A
B3S
6
-137.76
-11.99
27
A
LEU
9
-167.84
-51.77
27
A
THR
13
-160.03
101.36
Solution structure of beta3-analogue peptide corresponding to the gp41 600-612 loop of HIV.
1
N
N
disulf
2.100
A
CYS
5
A
SG
CYS
5
1_555
A
CYS
11
A
SG
CYS
11
1_555
covale
1.325
both
A
ACE
1
A
C
ACE
1
1_555
A
ILE
2
A
N
ILE
2
1_555
covale
1.337
both
A
CYS
5
A
C
CYS
5
1_555
A
B3S
6
A
N
B3S
6
1_555
covale
1.326
both
A
B3S
6
A
C
B3S
6
1_555
A
GLY
7
A
N
GLY
7
1_555
VIRAL PROTEIN
beta peptide, gp41, cyclic peptide, Viral protein
ENV_HV1BN
UNP
1
591
P12488
IWGCSGKLICTTA
591
603
1J8N
2
14
P12488
A
1
2
14
1
acetylation
ACE
1
1J8N
A
P12488
UNP
1
1
SER
engineered mutation
B3S
6
1J8N
A
P12488
UNP
595
6
BINDING SITE FOR RESIDUE ACE A 1
A
ACE
1
Software
2
A
ILE
2
A
ILE
2
2
1_555
A
B3S
6
A
B3S
6
2
1_555