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.
Petit, M.C.
Guichard, G.
Briand, J.P.
Muller, S.
Cung, M.T.
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 S
121.158
y
CYSTEINE
L-peptide linking
C6 H15 N4 O2 1
175.209
D-ARGININE
D-peptide linking
C5 H9 N O4
147.129
D-GLUTAMIC ACID
D-peptide linking
C6 H13 N O2
131.173
D-ISOLEUCINE
D-peptide linking
C4 H6 O4
118.088
METHYLMALONIC ACID
non-polymer
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
H2 N
16.023
AMINO GROUP
non-polymer
US
Biochemistry
BICHAW
0033
0006-2960
40
5720
5727
10.1021/bi001151h
11341837
Structure of antibody-bound peptides and retro-inverso analogues. A transferred nuclear Overhauser effect spectroscopy and molecular dynamics approach.
2001
10.2210/pdb1cwz/pdb
pdb_00001cwz
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
846.980
HISTONE H3
C-TERMINAL DOMAIN: Residues 130-135
1
syn
polymer
118.088
METHYLMALONIC ACID
1
syn
non-polymer
no
yes
(DAR)(DGL)G(DAR)(DIL)GGC(NH2)
REGRIGGCX
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1999-09-03
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_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_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1CS9 IS THE PARENT PEPTIDE
1CT6 IS A PARENT ANALOGUE PEPTIDE OF THE IREGERA SEQUENCE (IN THIS PEPTIDE,
ALA WAS REPLACED BY GLY).
1CVQ IS THE RETRO-INVERSO ANALOGUE OF 1CT6.
1CW8 IS THE RETRO-INVERSO ANALOGUE OF 1CS9, MODELLED WITH MR-A.
RCSB
Y
RCSB
1999-08-27
REL
DXX
METHYLMALONIC ACID
THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE CGG WAS ADDED AS A LINKER TO THE DEXTRAN MATRIX IN BIACORE EXPERIMENTS VIA THE CYS THIOL GROUP. NH2-CO WAS ADDED AT THE C-TERMINAL EXTREMITY OF THE RETRO-INVERSO PEPTIDE IN ORDER TO MIMIC THE N-TERMINAL OF THE PARENT PEPTIDE. ALL NON GLYCINE RESIDUE PRESENT A D-CONFIGURATION EXCEPT CYS. TWO RI(MA) DIASTEREISOMERS WERE OBTAINED AND COULDN'T BE SEPARATED.
sample
THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1(I.E. 5 MM OF PEPTIDE AND 0.1
MM OF MAB)
structures with the lowest energy
50
7
COSY, TOCSY, NOESY
0.1M PHOSPHATE
7
1
atm
277
K
THE STRUCTURES ARE BASED ON A SET OF 35 TO 60 BACKBONE-BACKBONE, BACKBONE-SIDE
CHAIN AND SIDE CHAIN-SIDE CHAIN DISTANCE RESTRAINTS. THE PHI ANGLE FOR THE NON
GLYCINE D-RESIDUES WAS CONSTRAINED BETWEEN 0 AND 175. A DISTANCE DEPENDENT
DIELECTRIC CONSTANT EQUAL TO 4R WAS APPLIED. THE NET ELECTRIC CHARGES WERE
DECREASED, WHILE THOSE OF THE N AND C-TERMINAL CHARGED GROUPS WERE NEGLECTED.
ENERGY MINIMISATION MOLECULAR DYNAMICS (SIMULATED ANNEALING)
6
lowest energy
5MM PEPTIDE, 0.1 MM MAB. 100 MM PHOSPHATE BUFFER CONTAINING 0.02% SODIUM AZIDE
GUNTERT, WUTHRICH
structure solution
DYANA
1.4
MOLECULAR SIMULATIONS INC.
structure solution
Discover
3
MOLECULAR SIMULATIONS INC.
refinement
Discover
3
400
Bruker
DRX
DXS
1
2
DXX
DXX
1
A
DAR
2
n
1
DAR
2
A
DGL
3
n
2
DGL
3
A
GLY
4
n
3
GLY
4
A
DAR
5
n
4
DAR
5
A
DIL
6
n
5
DIL
6
A
GLY
7
n
6
GLY
7
A
GLY
8
n
7
GLY
8
A
CYS
9
n
8
CYS
9
A
NH2
10
n
9
NH2
10
A
author_defined_assembly
1
monomeric
A
DAR
2
D-ARGININE
A
DAR
1
ARG
A
DGL
3
D-GLUTAMIC ACID
A
DGL
2
GLU
A
DAR
5
D-ARGININE
A
DAR
4
ARG
A
DIL
6
D-ISOLEUCINE
A
DIL
5
ILE
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
4
A
A
HG
HN2
CYS
NH2
9
10
1.14
6
A
A
O
HG
GLY
CYS
8
9
0.95
6
A
A
HA3
SG
GLY
CYS
4
9
1.16
6
A
A
CA
SG
GLY
CYS
4
9
1.91
6
A
A
O
SG
GLY
CYS
4
9
2.10
6
A
A
C
SG
GLY
CYS
4
9
2.15
7
A
A
CG
HG
DAR
CYS
5
9
0.93
7
A
A
HA
SG
DAR
CYS
5
9
1.00
7
A
A
HG2
HG
DAR
CYS
5
9
1.10
7
A
A
CB
HG
DAR
CYS
5
9
1.16
7
A
A
CA
SG
DAR
CYS
5
9
1.65
7
A
A
CB
SG
DAR
CYS
5
9
1.85
1
3.70
0.50
120.30
124.00
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
2
2
2
N
1
3.76
0.50
120.30
124.06
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
2
3.63
0.50
120.30
123.93
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
2
2
2
N
2
3.62
0.50
120.30
123.92
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
3
3.80
0.50
120.30
124.10
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
2
2
2
N
3
3.71
0.50
120.30
124.01
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
4
3.66
0.50
120.30
123.96
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
2
2
2
N
4
3.68
0.50
120.30
123.98
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
5
3.72
0.50
120.30
124.02
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
2
2
2
N
5
3.74
0.50
120.30
124.04
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
6
3.82
0.50
120.30
124.12
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
2
2
2
N
6
3.85
0.50
120.30
124.15
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
7
3.62
0.50
120.30
123.92
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
2
2
2
N
7
3.77
0.50
120.30
124.07
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
3
A
DIL
6
114.92
-70.67
7
A
DIL
6
83.06
75.04
Solution structure of the analogue retro-inverso (MA-S)REGRIGGC in contact with the monoclonal antibody MAB 4X11, NMR, 7 structures
1
N
N
2
N
N
A
DAR
2
A
DAR
1
HELX_P
A
GLY
7
A
GLY
6
1
1
6
covale
1.345
both
A
DXX
1
B
C
DXX
1_555
A
DAR
2
A
N
DAR
1
1_555
covale
1.355
both
A
DAR
2
A
C
DAR
1
1_555
A
DGL
3
A
N
DGL
2
1_555
covale
1.342
both
A
DGL
3
A
C
DGL
2
1_555
A
GLY
4
A
N
GLY
3
1_555
covale
1.350
both
A
GLY
4
A
C
GLY
3
1_555
A
DAR
5
A
N
DAR
4
1_555
covale
1.356
both
A
DAR
5
A
C
DAR
4
1_555
A
DIL
6
A
N
DIL
5
1_555
covale
1.349
both
A
DIL
6
A
C
DIL
5
1_555
A
GLY
7
A
N
GLY
6
1_555
covale
1.326
both
A
CYS
9
A
C
CYS
8
1_555
A
NH2
10
A
N
NH2
9
1_555
DNA BINDING PROTEIN
PSEUDOMIMETIC, SYNTHETIC PEPTIDE, RETRO-INVERSO ANALOGUE, TR-NOE, ANTIGEN- ANTIBODY COMPLEX, DNA BINDING PROTEIN
1CWZ
PDB
1
1CWZ
2
10
1CWZ
2
10
1CWZ
A
1
1
9
BINDING SITE FOR RESIDUE DXX A 1
A
DXX
1
Software
2
A
DAR
2
A
DAR
1
2
1_555
A
DGL
3
A
DGL
2
2
1_555
1
P 1