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SMTL ID : 1o3q.1
PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 3.00 Å
Oligo State
homo-dimer
Ligands
4 x
CMP
:
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
(Non-covalent)
CMP.1:
16 residues within 4Å:
Chain C:
V.42
,
L.54
,
S.55
,
I.63
,
G.64
,
E.65
,
L.66
,
G.67
,
R.75
,
S.76
,
A.77
,
V.79
,
R.116
,
T.120
Chain F:
L.117
,
S.121
13
PLIP interactions
:
12 interactions with chain C
,
1 interactions with chain F
Hydrogen bonds:
C:G.64
,
C:E.65
,
C:E.65
,
C:L.66
,
C:G.67
,
C:S.76
,
C:A.77
,
C:Y.92
,
C:R.116
,
C:T.120
,
F:S.121
Water bridges:
C:S.55
Salt bridges:
C:R.75
CMP.2:
13 residues within 4Å:
Chain B:
A.5
Chain C:
K.50
,
E.51
,
M.52
,
Q.163
,
G.166
,
Q.167
,
G.170
,
C.171
,
S.172
,
R.173
Chain F:
A.128
,
F.129
5
PLIP interactions
:
4 interactions with chain C
,
1 interactions with chain F
Hydrogen bonds:
C:E.51
,
C:Q.163
,
C:Q.167
,
C:R.173
,
F:A.128
CMP.3:
16 residues within 4Å:
Chain C:
L.117
,
S.121
Chain F:
V.42
,
L.54
,
S.55
,
I.63
,
G.64
,
E.65
,
L.66
,
G.67
,
R.75
,
S.76
,
A.77
,
V.79
,
R.116
,
T.120
14
PLIP interactions
:
13 interactions with chain F
,
1 interactions with chain C
Hydrogen bonds:
F:G.64
,
F:E.65
,
F:E.65
,
F:L.66
,
F:G.67
,
F:S.76
,
F:A.77
,
F:Y.92
,
F:R.116
,
F:T.120
,
F:T.120
,
C:S.121
Water bridges:
F:S.55
Salt bridges:
F:R.75
CMP.4:
13 residues within 4Å:
Chain C:
A.128
,
F.129
Chain E:
A.5
Chain F:
K.50
,
E.51
,
M.52
,
Q.163
,
G.166
,
Q.167
,
G.170
,
C.171
,
S.172
,
R.173
5
PLIP interactions
:
4 interactions with chain F
,
1 interactions with chain C
Hydrogen bonds:
F:E.51
,
F:Q.163
,
F:Q.167
,
F:R.173
,
C:A.128
Links
RCSB
PDBe
PDBj
PDBsum
CATH
PLIP
Citation
Chen, S. et al., Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking. J.Mol.Biol. (2001)
Release Date
2003-04-08
Peptides
CATABOLITE GENE ACTIVATOR PROTEIN:
C
F
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
C
A
F
A
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