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, 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/pdb1cw8/pdb
pdb_00001cw8
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 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 IRGERA sequence. (in this peptide, ALA was replaced by GLY).
1 CVQ is the retro-inverso analogue of 1CT6.
RCSB
Y
RCSB
1999-08-26
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 residues 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
6
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)
5
lowest energy
5 mM peptide, 0.1 mM mAb; 100 mM phosphate buffer containning 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
DXX
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
1
3.85
0.50
120.30
124.15
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
2
2
2
N
1
3.64
0.50
120.30
123.94
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
5
5
5
N
2
3.72
0.50
120.30
124.02
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
2
2
2
N
2
3.80
0.50
120.30
124.10
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
5
5
5
N
3
3.72
0.50
120.30
124.02
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
2
2
2
N
3
3.73
0.50
120.30
124.03
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
5
5
5
N
4
3.69
0.50
120.30
123.99
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
2
2
2
N
4
3.64
0.50
120.30
123.94
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
5
5
5
N
5
3.61
0.50
120.30
123.91
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
2
2
2
N
5
3.65
0.50
120.30
123.95
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
5
5
5
N
6
3.67
0.50
120.30
123.97
A
A
A
NE
CZ
NH2
DAR
DAR
DAR
2
2
2
N
6
3.84
0.50
120.30
124.14
A
A
A
NE
CZ
NH1
DAR
DAR
DAR
5
5
5
N
2
A
DIL
6
115.96
-69.49
3
A
DIL
6
153.26
-70.71
5
A
DIL
6
85.06
73.07
6
A
DIL
6
110.22
-66.85
SOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO (mA-R)REGRIGGC IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 6 STRUCTURES
1
N
N
2
N
N
covale
1.346
both
A
DXX
1
B
C
DXX
1_555
A
DAR
2
A
N
DAR
1
1_555
covale
1.357
both
A
DAR
2
A
C
DAR
1
1_555
A
DGL
3
A
N
DGL
2
1_555
covale
1.345
both
A
DGL
3
A
C
DGL
2
1_555
A
GLY
4
A
N
GLY
3
1_555
covale
1.354
both
A
GLY
4
A
C
GLY
3
1_555
A
DAR
5
A
N
DAR
4
1_555
covale
1.347
both
A
DAR
5
A
C
DAR
4
1_555
A
DIL
6
A
N
DIL
5
1_555
covale
1.346
both
A
DIL
6
A
C
DIL
5
1_555
A
GLY
7
A
N
GLY
6
1_555
covale
1.327
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
1CW8
PDB
1
1CW8
2
10
1CW8
2
10
1CW8
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