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
C2 H4 O
44.053
ACETYL GROUP
non-polymer
C3 H7 N O2
89.093
y
ALANINE
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
C4 H10 N2 O2
118.134
n
2,4-DIAMINOBUTYRIC ACID
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
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/pdb1j9v/pdb
pdb_00001j9v
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
1
1.0
1388.589
DabD (Ace)IWG(DAB)SGKLIDTTA ANALOGUE OF HIV GP41
1
syn
polymer
no
yes
(ACE)IWG(DAB)SGKLIDTTA
XIWGASGKLIDTTA
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-07-01
1
1
2008-04-27
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
THE 1IM7 entry contains the parent peptides coordinates.
The 1J8N entry contains the beta3-Ser analogue peptide (HSER)
The 1J8Z entry contains the beta3-Cys analogue peptide (HCYS)
RCSB
Y
RCSB
2001-05-29
REL
REL
The parent peptide (IWGCSGKLICTTA) occurs in HIV gp41 glycoprotein.
sample
This structure was determined using standard 2D homonuclear techniques. Different NOESY experiments with mixing times from 80 ms to 800 ms were recorded, in order to determined the best conditions avoiding spin diffusion.
target function
50
49
DQF-COSY
2D NOESY
TOCSY
ambient
298
K
50 INITIAL RANDOM STRUCTURES WERE GENERATED USING SIMULATED ANNEALING IN DYANA SOFTWARE, FOLLOWED BY 500PS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K, 200 PS MD UNDER NMR RESTRAINTS AND 750 STEPS CONJUGATED GRADIENT EM USING DISCOVER OF MSI SOFTWARE
Torsion angle dinamics, molecular dynamics, energy minimization.
1
lowest energy
3,5 mM peptide in 500ul DMSO-D6
DMSO-D6
Bruker GMBH
collection
XwinNMR
2.6
Bruker GMBH
processing
XwinNMR
2.6
Bartels C., Xia T., Billeter M., Guentert P. and Wuethrich K. (1995) J. Biomol. NMR, 5, 1-10
data analysis
XEASY
1.2
Guentert P., Mumenthaler C. and Wuethrich K. (1997) J. Mol. Biol. 273, 283-298
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
DAB
5
n
5
DAB
5
A
SER
6
n
6
SER
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
ASP
11
n
11
ASP
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
A
DAB
5
2,4-DIAMINOBUTYRIC ACID
A
DAB
5
ALA
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
1
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
2
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
3
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
4
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
5
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
6
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
7
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
8
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
9
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
10
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
11
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
12
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
13
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
14
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
15
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
16
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
17
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
18
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
19
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
20
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
21
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
22
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
23
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
24
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
25
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
26
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
27
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
28
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
29
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
30
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
31
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
32
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
33
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
34
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
35
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
36
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
37
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
38
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
39
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
40
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
41
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
42
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
43
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
44
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
45
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
46
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
47
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
48
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
49
A
OD2
ASP
11
A
OD2
ASP
11
1
Y
1
A
A
ND
CG
DAB
ASP
5
11
1.34
2
A
A
ND
CG
DAB
ASP
5
11
1.34
3
A
A
ND
CG
DAB
ASP
5
11
1.34
4
A
A
ND
CG
DAB
ASP
5
11
1.34
5
A
A
ND
CG
DAB
ASP
5
11
1.34
6
A
A
ND
CG
DAB
ASP
5
11
1.34
7
A
A
ND
CG
DAB
ASP
5
11
1.34
8
A
A
ND
CG
DAB
ASP
5
11
1.34
9
A
A
ND
CG
DAB
ASP
5
11
1.34
10
A
A
ND
CG
DAB
ASP
5
11
1.34
11
A
A
ND
CG
DAB
ASP
5
11
1.34
12
A
A
ND
CG
DAB
ASP
5
11
1.35
13
A
A
ND
CG
DAB
ASP
5
11
1.34
14
A
A
ND
CG
DAB
ASP
5
11
1.34
15
A
A
ND
CG
DAB
ASP
5
11
1.35
16
A
A
ND
CG
DAB
ASP
5
11
1.35
17
A
A
ND
CG
DAB
ASP
5
11
1.34
18
A
A
ND
CG
DAB
ASP
5
11
1.34
19
A
A
ND
CG
DAB
ASP
5
11
1.34
20
A
A
ND
CG
DAB
ASP
5
11
1.34
21
A
A
ND
CG
DAB
ASP
5
11
1.34
22
A
A
ND
CG
DAB
ASP
5
11
1.34
23
A
A
ND
CG
DAB
ASP
5
11
1.34
24
A
A
ND
CG
DAB
ASP
5
11
1.34
25
A
A
ND
CG
DAB
ASP
5
11
1.34
26
A
A
ND
CG
DAB
ASP
5
11
1.34
27
A
A
ND
CG
DAB
ASP
5
11
1.34
28
A
A
ND
CG
DAB
ASP
5
11
1.34
29
A
A
ND
CG
DAB
ASP
5
11
1.34
30
A
A
ND
CG
DAB
ASP
5
11
1.34
31
A
A
ND
CG
DAB
ASP
5
11
1.34
32
A
A
ND
CG
DAB
ASP
5
11
1.34
33
A
A
ND
CG
DAB
ASP
5
11
1.34
34
A
A
ND
CG
DAB
ASP
5
11
1.34
35
A
A
ND
CG
DAB
ASP
5
11
1.34
36
A
A
ND
CG
DAB
ASP
5
11
1.35
37
A
A
ND
CG
DAB
ASP
5
11
1.34
38
A
A
ND
CG
DAB
ASP
5
11
1.34
39
A
A
ND
CG
DAB
ASP
5
11
1.34
40
A
A
ND
CG
DAB
ASP
5
11
1.35
41
A
A
ND
CG
DAB
ASP
5
11
1.35
42
A
A
ND
CG
DAB
ASP
5
11
1.34
43
A
A
ND
CG
DAB
ASP
5
11
1.34
44
A
A
ND
CG
DAB
ASP
5
11
1.35
45
A
A
ND
CG
DAB
ASP
5
11
1.34
46
A
A
ND
CG
DAB
ASP
5
11
1.35
47
A
A
ND
CG
DAB
ASP
5
11
1.35
48
A
A
ND
CG
DAB
ASP
5
11
1.34
49
A
A
ND
CG
DAB
ASP
5
11
1.34
1
A
A
C
OXT
ALA
ALA
14
14
0.152
0.019
1.229
1.381
N
2
A
A
C
OXT
ALA
ALA
14
14
0.152
0.019
1.229
1.381
N
3
A
A
C
OXT
ALA
ALA
14
14
0.154
0.019
1.229
1.383
N
4
A
A
C
OXT
ALA
ALA
14
14
0.155
0.019
1.229
1.384
N
5
A
A
C
OXT
ALA
ALA
14
14
0.155
0.019
1.229
1.384
N
6
A
A
C
OXT
ALA
ALA
14
14
0.154
0.019
1.229
1.383
N
7
A
A
C
OXT
ALA
ALA
14
14
0.155
0.019
1.229
1.384
N
8
A
A
C
OXT
ALA
ALA
14
14
0.154
0.019
1.229
1.383
N
9
A
A
C
OXT
ALA
ALA
14
14
0.154
0.019
1.229
1.383
N
10
A
A
C
OXT
ALA
ALA
14
14
0.153
0.019
1.229
1.382
N
11
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
12
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
13
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
14
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
15
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
16
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
17
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
18
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
19
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
20
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
21
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
22
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
23
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
24
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
25
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
26
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
27
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
28
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
29
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
30
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
31
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
32
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
33
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
34
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
35
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
36
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
37
A
A
C
OXT
ALA
ALA
14
14
0.146
0.019
1.229
1.375
N
38
A
A
C
OXT
ALA
ALA
14
14
0.146
0.019
1.229
1.375
N
39
A
A
C
OXT
ALA
ALA
14
14
0.147
0.019
1.229
1.376
N
40
A
A
C
OXT
ALA
ALA
14
14
0.147
0.019
1.229
1.376
N
41
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
42
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
43
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
44
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
45
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
46
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
47
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
48
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
49
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
1
A
LYS
8
-157.16
-67.51
2
A
LYS
8
-156.97
-67.63
3
A
LYS
8
-157.02
-67.46
4
A
LYS
8
-159.50
-66.57
5
A
LYS
8
-159.12
-66.55
6
A
LYS
8
-158.59
-67.53
7
A
LYS
8
-158.82
-67.31
8
A
LYS
8
-163.59
-61.20
9
A
LYS
8
-159.39
-66.85
10
A
LYS
8
-157.50
-66.66
11
A
LYS
8
-158.03
-67.73
11
A
THR
12
-94.06
-69.17
12
A
LYS
8
-142.69
-80.98
12
A
ASP
11
-109.95
76.44
13
A
LYS
8
-156.63
-70.38
14
A
LYS
8
-159.28
-68.09
14
A
THR
12
-98.78
-83.32
15
A
LYS
8
-150.88
-72.28
15
A
ASP
11
-108.48
75.50
15
A
THR
12
-80.52
-79.95
16
A
LYS
8
-139.82
-80.08
16
A
ASP
11
-103.81
73.42
17
A
LYS
8
-158.39
-68.65
17
A
THR
12
-97.41
-81.80
18
A
LYS
8
-146.55
-79.26
19
A
LYS
8
-159.06
-68.84
19
A
THR
12
-98.39
-83.29
20
A
LYS
8
-159.05
-68.66
21
A
SER
6
-98.00
-70.17
21
A
LYS
8
-150.27
-72.11
21
A
THR
12
-132.86
-57.86
22
A
SER
6
-110.65
-76.21
22
A
LYS
8
-132.15
-68.49
23
A
SER
6
-112.71
-75.32
23
A
LYS
8
-146.68
-71.60
24
A
SER
6
-95.70
-75.35
24
A
LYS
8
-142.80
-73.56
24
A
THR
12
-152.49
-52.12
24
A
THR
13
-128.21
-59.09
25
A
SER
6
-95.34
-75.85
25
A
LYS
8
-135.72
-68.88
25
A
THR
12
-156.91
-50.40
26
A
LYS
8
-159.35
-64.87
26
A
THR
12
-158.28
-46.01
26
A
THR
13
-131.88
-64.74
27
A
LYS
8
-161.89
-57.88
27
A
THR
12
-151.09
-70.71
27
A
THR
13
-102.70
-66.12
28
A
LYS
8
-162.36
-57.60
28
A
THR
12
-152.07
-68.92
28
A
THR
13
-103.54
-66.56
29
A
LYS
8
-158.31
-66.28
29
A
THR
12
-158.06
-50.81
30
A
LYS
8
-158.56
-65.66
30
A
THR
12
-158.12
-46.05
30
A
THR
13
-130.42
-66.77
31
A
LYS
8
-158.15
-66.24
31
A
THR
12
-158.16
-47.07
31
A
THR
13
-131.12
-64.90
32
A
LYS
8
-157.71
-66.78
32
A
THR
12
-158.95
-47.34
32
A
THR
13
-126.55
-67.82
33
A
LYS
8
-156.92
-64.64
33
A
ASP
11
-116.14
65.51
33
A
THR
12
-156.01
-75.85
34
A
LYS
8
-158.82
-62.74
34
A
THR
12
-140.43
-65.85
35
A
SER
6
-154.33
78.50
35
A
LYS
8
-153.23
-74.94
36
A
LYS
8
-152.47
-74.18
37
A
SER
6
-154.95
81.21
37
A
LYS
8
-152.80
-75.28
38
A
SER
6
-154.90
80.46
38
A
LYS
8
-152.28
-75.32
39
A
SER
6
-156.11
82.03
39
A
LYS
8
-152.36
-74.90
40
A
SER
6
-163.22
81.52
40
A
LYS
8
-139.33
-80.22
41
A
SER
6
-161.35
79.51
41
A
LYS
8
-137.33
-80.98
42
A
LYS
8
-159.02
-67.73
43
A
LYS
8
-154.63
-69.25
43
A
THR
12
-73.62
-72.60
44
A
LYS
8
-153.49
-70.91
44
A
ASP
11
-116.41
68.93
44
A
THR
12
-152.76
-54.36
45
A
LYS
8
-154.92
-70.41
45
A
ASP
11
-119.18
69.99
45
A
THR
12
-155.19
-68.48
46
A
LYS
8
-154.95
-70.29
46
A
ASP
11
-119.68
70.16
46
A
THR
12
-154.24
-66.13
47
A
TRP
3
-149.77
22.76
47
A
SER
6
-151.91
81.69
47
A
LYS
8
-137.07
-77.79
47
A
LEU
9
-115.29
60.64
47
A
ASP
11
-114.17
75.00
47
A
THR
12
-145.51
-82.78
48
A
LYS
8
-158.42
-65.43
48
A
ASP
11
-105.79
71.53
49
A
LYS
8
-159.82
-67.84
Solution structure of a lactam analogue (DabD) of HIV gp41 600-612 loop.
1
N
N
covale
1.340
both
A
ACE
1
A
C
ACE
1
1_555
A
ILE
2
A
N
ILE
2
1_555
covale
1.347
both
A
GLY
4
A
C
GLY
4
1_555
A
DAB
5
A
N
DAB
5
1_555
covale
1.344
both
A
DAB
5
A
C
DAB
5
1_555
A
SER
6
A
N
SER
6
1_555
VIRAL PROTEIN
lactam peptide, lactam bond, HIV, gp41, cyclic peptide, Viral protein
ENV_HV1BN
UNP
1
591
P12488
IWGCSGKLICTTA
591
603
1J9V
2
14
P12488
A
1
2
14
1
insertion
ACE
1
1J9V
A
P12488
UNP
1
1
CYS
engineered mutation
DAB
5
1J9V
A
P12488
UNP
594
5
1
CYS
engineered mutation
ASP
11
1J9V
A
P12488
UNP
600
11