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 H10 N2 O2
118.134
n
2,4-DIAMINOBUTYRIC ACID
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 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/pdb1jdk/pdb
pdb_00001jdk
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
1402.615
ACETYL GROUP
1
syn
polymer
no
yes
(ACE)IWGESGKLI(DAB)TTA
XIWGESGKLIATTA
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
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
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_conn.pdbx_leaving_atom_flag
1IM7 contains the parent peptide AcIWGCSGKLICTTA.
1J8N contains a beta3-Ser containing analogue peptide (HSER)
1J8Z contains a beta3-Cys containing analogue peptide (HCYS)
1J9V contains the lactam analogue DabD
1JAR contains the lactam analogue peptide DDab
1JC8 contains the lactam analogue peptide DDap
1JAA contains the lactam analogue peptide DapE
1JCP contains the lactam analogue peptide EDap
1JD8 contains the lactam analogue peptide DapD
RCSB
Y
RCSB
2001-06-14
REL
REL
the parent peptide IWGCSGKLICTTA occurs naturally in HIV gp41 glycoprotein
sample
Typical 2D ho;onuclear techniques were applied. Different NOESY experiment with different mixing times (from 80ms to 800ms) were recorded in order to determine the best conditions without spin diffusion.
target function
50
25
2D NOESY
DQF-COSY
TOCSY
atmospheric
atm
298
K
50 initial random strucutre were generated using DYANA software, followed by 500 steps energy minimization. Then using DISCOVER 3 35 ps MD in vacuo at 300K, 200 steps energy minimization under NMR restraints and 750 steps conjugate gradient EM.
torsion angle dynamics, energy minimization, molecular dynamics
1
lowest energy
3mMpeptide in 500ul solvent
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 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
MSI, 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
GLU
5
n
5
GLU
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
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
2
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
3
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
4
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
5
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
6
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
7
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
8
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
9
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
10
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
11
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
12
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
13
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
14
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
15
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
16
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
17
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
18
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
19
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
20
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
21
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
22
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
23
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
24
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
25
A
OE2
GLU
5
A
OE2
GLU
5
1
Y
1
A
A
CD
ND
GLU
DAB
5
11
1.34
2
A
A
CD
ND
GLU
DAB
5
11
1.34
3
A
A
CD
ND
GLU
DAB
5
11
1.34
4
A
A
CD
ND
GLU
DAB
5
11
1.35
5
A
A
CD
ND
GLU
DAB
5
11
1.34
6
A
A
CD
ND
GLU
DAB
5
11
1.34
7
A
A
CD
ND
GLU
DAB
5
11
1.34
8
A
A
CD
ND
GLU
DAB
5
11
1.34
9
A
A
CD
ND
GLU
DAB
5
11
1.34
10
A
A
CD
ND
GLU
DAB
5
11
1.34
11
A
A
CD
ND
GLU
DAB
5
11
1.34
12
A
A
CD
ND
GLU
DAB
5
11
1.34
13
A
A
CD
ND
GLU
DAB
5
11
1.34
14
A
A
CD
ND
GLU
DAB
5
11
1.34
15
A
A
CD
ND
GLU
DAB
5
11
1.34
16
A
A
CD
ND
GLU
DAB
5
11
1.35
17
A
A
CD
ND
GLU
DAB
5
11
1.35
18
A
A
CD
ND
GLU
DAB
5
11
1.34
19
A
A
CD
ND
GLU
DAB
5
11
1.34
20
A
A
CD
ND
GLU
DAB
5
11
1.35
21
A
A
CD
ND
GLU
DAB
5
11
1.34
22
A
A
CD
ND
GLU
DAB
5
11
1.34
23
A
A
CD
ND
GLU
DAB
5
11
1.34
24
A
A
CD
ND
GLU
DAB
5
11
1.34
25
A
A
CD
ND
GLU
DAB
5
11
1.34
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
0.146
0.019
1.229
1.375
N
3
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
4
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
5
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
6
A
A
C
OXT
ALA
ALA
14
14
0.146
0.019
1.229
1.375
N
7
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
8
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
9
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
N
10
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
11
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
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
0.145
0.019
1.229
1.374
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
0.147
0.019
1.229
1.376
N
16
A
A
C
OXT
ALA
ALA
14
14
0.144
0.019
1.229
1.373
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
0.141
0.019
1.229
1.370
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
0.141
0.019
1.229
1.370
N
22
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
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
0.144
0.019
1.229
1.373
N
25
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
1
A
SER
6
-136.00
-109.87
1
A
LEU
9
-147.49
-71.50
2
A
THR
12
-163.52
115.63
3
A
LYS
8
-153.29
-58.66
3
A
LEU
9
-69.47
-72.09
3
A
DAB
11
-169.43
101.45
4
A
THR
12
-124.75
-88.23
5
A
SER
6
-138.44
-115.97
5
A
LYS
8
-129.15
-83.52
5
A
LEU
9
-97.36
-71.49
5
A
THR
12
-80.67
-92.05
6
A
LEU
9
-140.15
-58.92
7
A
SER
6
-86.19
-116.74
7
A
LYS
8
-110.64
-163.60
8
A
LYS
8
-91.36
-68.88
8
A
LEU
9
-145.99
-66.08
9
A
LEU
9
-121.78
-83.99
9
A
THR
12
-141.39
-72.17
10
A
GLU
5
-133.74
-33.89
11
A
SER
6
-150.06
-138.21
11
A
LYS
8
-143.84
-68.29
11
A
LEU
9
-115.39
-71.43
12
A
LEU
9
-149.58
-59.84
13
A
LYS
8
-97.71
-70.81
13
A
LEU
9
-141.67
-68.59
14
A
SER
6
-136.69
-126.32
15
A
THR
12
-124.53
-74.52
15
A
THR
13
-133.25
-61.55
16
A
SER
6
-127.02
-129.05
16
A
LYS
8
-143.90
-76.64
16
A
LEU
9
-125.89
-80.07
17
A
LEU
9
-78.29
-75.96
18
A
THR
13
-91.37
-63.36
19
A
GLU
5
-103.90
59.52
19
A
SER
6
-179.10
-97.02
19
A
LYS
8
-147.83
-57.97
19
A
LEU
9
-128.55
-72.89
20
A
LEU
9
-126.47
-98.22
20
A
THR
12
-126.17
-72.63
21
A
LYS
8
-98.46
-80.91
21
A
LEU
9
-118.64
-72.63
22
A
GLU
5
-118.51
72.31
22
A
SER
6
-163.14
87.65
23
A
SER
6
-141.23
-121.47
25
A
SER
6
-130.29
-113.01
solution structure of lactam analogue (EDap) 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
1.352
both
A
ILE
10
A
C
ILE
10
1_555
A
DAB
11
A
N
DAB
11
1_555
covale
1.359
both
A
DAB
11
A
C
DAB
11
1_555
A
THR
12
A
N
THR
12
1_555
VIRAL PROTEIN
cyclic peptide, peptidomimetics, HIV, gp41, lactam bond, Viral protein
1JDK
PDB
1
1JDK
1
14
1JDK
1
14
1JDK
A
1
1
14