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/pdb1jar/pdb
pdb_00001jar
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
DDab: (ACE)IWGDSGKLI(DAB)TTA ANALOGUE OF HIV GP41
1
man
polymer
no
yes
(ACE)IWGDSGKLI(DAB)TTA
XIWGDSGKLIATTA
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_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
The 1IM7 entry contains the parent peptide.
The 1J8N entry contains the beta3-SER containg analogue (HSER)
The 1J8Z entry contains the beta3-Cys containg analogue peptide (HCYS)
The 1J9V entry contains the lactam analogue DabD
The 1JAA entry contains the lactam analogue DapE
RCSB
Y
RCSB
2001-05-31
REL
REL
The parent peptide (IWGCSGKLICTTA) occurs naturaly in HIV gp41 glycoprotein.
sample
the structure was calculated using standard 2D homonuclear techniques. Different NOSY experiments were recorded in order to determined the best conditions avoiding spin diffusion
target function
50
49
2D NOESY
DQF-COSY
TOCSY
none
ambient
298
K
50 initial radom structure are generated using DYANA software.followed by 500 ps restrained minimization. Followed by 750 ps conjugated gradient EM using the DISCOVER module of MSI software.
torsion angle dynalmics, molecular dynanmics, energy minimization
1
lowest energy
4mM peptide in 500ul DMSO-D6
100% DMSO-D6
Bruker GMBH
collection
XwinNMR
2.6
Bruker GMBH
processing
XwinNMR
2.6
Bartels C., Xia T., Billeter M.,Guentert P. and Wuethrich (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
ASP
5
n
5
ASP
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
DAB
11
n
11
DAB
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
11
2,4-DIAMINOBUTYRIC ACID
A
DAB
11
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
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
2
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
3
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
4
A
A
C
OXT
ALA
ALA
14
14
0.146
0.019
1.229
1.375
N
5
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
6
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
7
A
A
C
OXT
ALA
ALA
14
14
0.146
0.019
1.229
1.375
N
8
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
9
A
A
C
OXT
ALA
ALA
14
14
0.147
0.019
1.229
1.376
N
10
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
11
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
12
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
13
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
14
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
15
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
16
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
17
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
18
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
19
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
20
A
A
C
OXT
ALA
ALA
14
14
0.146
0.019
1.229
1.375
N
21
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
22
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
23
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
24
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
25
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
26
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
27
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
28
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
29
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
30
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
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
0.141
0.019
1.229
1.370
N
33
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
34
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
35
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
36
A
A
C
OXT
ALA
ALA
14
14
0.146
0.019
1.229
1.375
N
37
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
38
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
39
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
40
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
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
0.144
0.019
1.229
1.373
N
44
A
A
C
OXT
ALA
ALA
14
14
0.146
0.019
1.229
1.375
N
45
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
46
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
47
A
A
C
OXT
ALA
ALA
14
14
0.147
0.019
1.229
1.376
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
0.144
0.019
1.229
1.373
N
1
A
THR
12
-72.69
-85.21
2
A
THR
13
-124.50
-73.70
7
A
THR
13
-91.55
-69.90
12
A
ILE
10
-158.28
82.02
15
A
TRP
3
-112.32
68.49
19
A
ILE
10
-154.11
83.68
20
A
SER
6
-158.93
85.72
20
A
ILE
10
-152.46
86.40
22
A
TRP
3
-114.01
50.80
22
A
ILE
10
-156.40
86.09
23
A
SER
6
-156.24
85.84
30
A
ILE
10
-163.59
70.52
31
A
ILE
10
-163.23
70.19
32
A
ILE
10
-161.66
69.93
33
A
ILE
10
-160.61
68.88
34
A
ILE
10
-164.74
70.57
35
A
ILE
10
-162.41
70.78
36
A
ILE
10
-160.03
67.77
37
A
ILE
10
-161.85
67.93
38
A
ILE
10
-154.40
72.26
39
A
ILE
10
-160.40
81.67
40
A
ILE
10
-161.34
80.08
41
A
ILE
10
-158.12
74.14
42
A
ILE
10
-163.07
68.41
43
A
ILE
10
-151.54
75.33
43
A
DAB
11
-104.22
61.24
45
A
ILE
10
-145.05
55.61
46
A
ILE
10
-161.25
73.12
47
A
ILE
10
-159.09
75.44
47
A
DAB
11
-105.06
52.81
48
A
ILE
10
-151.42
77.99
48
A
DAB
11
-115.52
69.67
49
A
ILE
10
-162.07
77.18
49
A
DAB
11
-112.14
71.59
Solution structure of lactam analogue (DDab)of HIV gp41 600-612 loop.
1
N
N
covale
1.341
both
A
ACE
1
A
C
ACE
1
1_555
A
ILE
2
A
N
ILE
2
1_555
covale
1.342
none
A
ASP
5
A
CG
ASP
5
1_555
A
DAB
11
A
ND
DAB
11
1_555
covale
1.353
both
A
ILE
10
A
C
ILE
10
1_555
A
DAB
11
A
N
DAB
11
1_555
covale
1.357
both
A
DAB
11
A
C
DAB
11
1_555
A
THR
12
A
N
THR
12
1_555
VIRAL PROTEIN
lactam bond, cyclic peptide, HIV gp41, peptidomimetics., Viral protein
ENV_HV1BN
UNP
1
591
P12488
IWGCSGKLICTTA
591
603
1JAR
2
14
P12488
A
1
2
14
1
acetylation
ACE
1
1JAR
A
P12488
UNP
1
1
CYS
engineered mutation
ASP
5
1JAR
A
P12488
UNP
594
5
1
CYS
engineered mutation
DAB
11
1JAR
A
P12488
UNP
600
11