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
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
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
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/pdb1cs9/pdb
pdb_00001cs9
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
920.050
HISTONE H3 PEPTIDE
C-TERMINAL REGION 130-135
1
syn
polymer
no
no
CGGIRGERA
CGGIRGERA
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
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
RCSB
Y
RCSB
1999-08-18
REL
THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE PEPTIDE CORRESPONDS TO THE IRGERA SEQUENCE PRESENT IN THE C-TERMINAL REGION 130-135 OF HISTONE H3 BOUND TO THE MAB 4X11 MONOCLONAL ANTIBODY (IGG1). THE SEQUENCE CGG WAS ADDED TO THE N- TERMINUS OF THE IRGERA SEQUENCE AS A LINKER TO THE DEXTRAN MATRIX IN BIACORE EXPERIMENTS VIA THE CYS THIOL GROUP.
sample
THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1 (I.E. 5MM OF PEPTIDE AND
0.1MM OF MAB)
structures with the lowest energy
50
7
TOCSY, NOESY, COSY
0.1M PHOSPHATE
7
1
atm
277
K
ENERGY MINIMISATION. A DISTANT 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. IN THE PDB, NH3+ IS INCLUDED IN THE RESIDUE CYS, AND
COO- IS INCLUDED IN THE RESIDUE ALA. THE RESIDUE GLU HAS MISSING ATOMS HE2 IN ALL STRUCTURES
BECAUSE IN DISCOVER, THIS RESIDUE IS MODELLED AS A CHARGED GROUP(WE HAVE COO- AND NOT COOH).
ENERGY MINIMIZATION MOLECULAR DYNAMICS
7
lowest energy
5 MM PEPTIDE, 0.1MM MAB; 100 MM PHOSPHATE BUFFER CONTAINING 0.02% SODIUM AZIDE
GUNTERT, WUTHRICH
structure solution
DYANA
1.4
MOLECULAR SIMULATIONS INC., SAN DIEGO, CA
structure solution
Discover
3
MOLECULAR SIMULATIONS INC.
refinement
Discover
3
400
Bruker
DRX
CYS
1
n
1
CYS
1
A
GLY
2
n
2
GLY
2
A
GLY
3
n
3
GLY
3
A
ILE
4
n
4
ILE
4
A
ARG
5
n
5
ARG
5
A
GLY
6
n
6
GLY
6
A
GLU
7
n
7
GLU
7
A
ARG
8
n
8
ARG
8
A
ALA
9
n
9
ALA
9
A
author_defined_assembly
1
monomeric
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
3.72
0.50
120.30
124.02
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
5
5
5
N
1
3.69
0.50
120.30
123.99
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
8
8
8
N
2
3.83
0.50
120.30
124.13
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
5
5
5
N
2
3.78
0.50
120.30
124.08
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
8
8
8
N
3
3.76
0.50
120.30
124.06
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
5
5
5
N
3
3.72
0.50
120.30
124.02
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
8
8
8
N
4
3.88
0.50
120.30
124.18
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
5
5
5
N
4
3.77
0.50
120.30
124.07
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
8
8
8
N
5
3.80
0.50
120.30
124.10
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
5
5
5
N
5
3.83
0.50
120.30
124.13
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
8
8
8
N
6
3.74
0.50
120.30
124.04
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
5
5
5
N
6
3.69
0.50
120.30
123.99
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
8
8
8
N
7
3.74
0.50
120.30
124.04
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
5
5
5
N
7
3.53
0.50
120.30
123.83
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
8
8
8
N
2
A
ARG
5
-154.01
-97.81
3
A
GLU
7
-158.65
-96.90
3
A
ARG
8
-160.87
65.11
4
A
ARG
5
-158.30
85.41
4
A
GLU
7
-163.13
119.21
4
A
ARG
8
-156.61
89.73
5
A
ARG
5
-157.65
-81.59
5
A
GLU
7
-157.47
-84.79
5
A
ARG
8
-157.62
-66.04
6
A
GLU
7
-155.53
83.01
7
A
GLU
7
-160.49
111.28
7
A
ARG
8
-151.36
85.82
SOLUTION STRUCTURE OF CGGIRGERA IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 7 STRUCTURES
1
N
N
DNA BINDING PROTEIN
SYNTHETIC PEPTIDE, TR-NOE, ANTIGEN-ANTIBODY COMPLEX, DNA BINDING PROTEIN
H31_HUMAN
UNP
1
P16106
130
135
1CS9
4
9
P16106
A
1
4
9
1
P 1