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
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C9 H17 N4 O5 1
261.255
n
2-(2-CARBOXY-ACETYLAMINO)-5-GUANIDINO-PENTANOIC ACID
D-ARGININE WITH 3-OXO-PROPIONIC ACID MODIFICATION
L-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/pdb1cvq/pdb
pdb_00001cvq
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
933.026
HISTONE H3
C-TERMINAL DOMAIN 130-135
1
syn
polymer
no
yes
(MGG)(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
1999-09-02
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_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1CS9 is the parent peptide of the original sequence of IRGERA.
1CT6 is the parent peptide, an analogue peptide of the IRGERA sequence. (In this peptide, ALA was replaced by GLY).
RCSB
Y
RCSB
1999-08-24
REL
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 residues present a D-configuration except CYS.
sample
THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1 (I.E. 5 MM OF PEPTIDE AND 0.1 MM 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)
7
lowest energy
5 mM peptide, 0.1 mM mAb; 100 mM phosphate buffer containing 0.02% sodium azide
95% H2O/5% D2O
Guntert, Wuthrich
structure solution
DYANA
1.4
Molecular Simulations Inc., San Diego, CA
structure solution
Discover
3
Molecular Simulations Inc., San Diego, CA
refinement
Discover
3
Bruker
collection
XwinNMR
1.2
400
Bruker
DRX
DAR
2
n
1
MGG
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
MGG
2
A
MGG
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
1
3.75
0.50
120.30
124.05
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
2
3.95
0.50
120.30
124.25
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
3
3.85
0.50
120.30
124.15
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
4
3.88
0.50
120.30
124.18
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
5
3.79
0.50
120.30
124.09
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
6
3.88
0.50
120.30
124.18
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
5
5
5
N
7
3.75
0.50
120.30
124.05
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
5
5
5
N
1
A
DIL
6
71.06
72.99
5
A
DIL
6
91.15
76.22
6
A
DIL
6
91.31
78.58
7
A
DIL
6
102.80
-65.70
SOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO MGREGRIGGC IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 7 STRUCTURES
1
N
N
covale
1.358
both
A
MGG
2
A
C
MGG
1
1_555
A
DGL
3
A
N
DGL
2
1_555
covale
1.346
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
1.348
both
A
DAR
5
A
C
DAR
4
1_555
A
DIL
6
A
N
DIL
5
1_555
covale
1.342
both
A
DIL
6
A
C
DIL
5
1_555
A
GLY
7
A
N
GLY
6
1_555
covale
1.330
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
1CVQ
PDB
1
1CVQ
2
10
1CVQ
2
10
1CVQ
A
1
1
9
BINDING SITE FOR RESIDUE NH2 A 10
A
NH2
10
Software
1
A
CYS
9
A
CYS
8
1
1_555
1
P 1