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SMTL ID : 4zmm.1
GGDEF domain of Dcsbis complexed with c-di-GMP
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.50 Å
Oligo State
homo-dimer
Ligands
2 x
C2E
:
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
(Non-covalent)
C2E.1:
18 residues within 4Å:
Chain A:
A.131
,
L.132
,
R.133
,
D.136
,
V.150
,
R.151
,
R.153
,
E.157
,
M.160
,
I.161
,
R.164
Chain B:
A.130
,
A.131
,
L.132
,
R.133
,
P.134
,
R.164
Ligands:
C2E.2
17
PLIP interactions
:
13 interactions with chain A
,
4 interactions with chain B
Hydrogen bonds:
A:R.133
,
A:R.133
,
A:R.151
,
A:R.164
,
A:R.164
,
B:L.132
,
B:R.133
,
B:R.164
,
B:R.164
Water bridges:
A:R.133
,
A:R.133
,
A:R.151
Salt bridges:
A:R.133
,
A:D.136
,
A:R.153
pi-Cation interactions:
A:R.133
,
A:R.133
C2E.2:
17 residues within 4Å:
Chain A:
A.130
,
A.131
,
L.132
,
R.133
,
P.134
,
R.164
Chain B:
L.132
,
R.133
,
D.136
,
V.150
,
R.151
,
R.153
,
E.157
,
M.160
,
I.161
,
R.164
Ligands:
C2E.1
15
PLIP interactions
:
11 interactions with chain B
,
4 interactions with chain A
Hydrogen bonds:
B:R.133
,
B:R.151
,
B:R.164
,
B:R.164
,
A:L.132
,
A:R.133
,
A:R.164
Water bridges:
B:R.133
,
B:R.133
,
B:R.151
Salt bridges:
B:R.133
,
B:D.136
,
B:R.153
pi-Cation interactions:
B:R.133
,
A:R.164
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Chen, Y. et al., Crystal structure of Dcsbis GGDEF domain complexed with c-di-GMP. To Be Published
Release Date
2016-05-04
Peptides
diguanylate cyclase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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