SMTL ID : 4xj6.1

Crystal structure of Escherichia coli DncV 3'-deoxy GTP bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.112, D.129, D.131 Ligands: MG.2, GH3.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.129, A:D.131, H2O.4 MG.2: 6 residues within 4Å: Chain A: D.129, D.131, D.191 Ligands: MG.1, GH3.3, GH3.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.129, A:D.129, A:D.131, A:D.191, H2O.4

2 x GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GH3.3: 19 residues within 4Å: Chain A: Q.110, G.111, S.112, Y.115, L.118, D.129, D.131, P.257, V.260, K.283, R.286, S.297, I.298, S.339, D.344, L.348 Ligands: MG.1, MG.2, GH3.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:Q.110, A:S.112, A:S.112, A:Y.115, A:P.257, A:R.286, A:S.297, A:S.339, A:S.339 Water bridges: A:F.113, A:T.117, A:D.129, A:E.261, A:K.283, A:K.283, A:I.298, A:S.339, A:D.344 Salt bridges: A:K.283, A:K.283, A:D.344 GH3.4: 12 residues within 4Å: Chain A: Q.110, D.131, K.175, T.177, C.178, D.191, Y.195, L.243, S.255, P.257 Ligands: MG.2, GH3.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.110, A:N.176, A:T.177, A:Y.195, A:Y.195, A:S.255, A:S.255 Salt bridges: A:K.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato, K. et al., Structural Basis for the Catalytic Mechanism of DncV, Bacterial Homolog of Cyclic GMP-AMP Synthase. Structure (2015)

Release Date

2015-04-29

Peptides

VC0179-like protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

VC0179-like protein