SMTL ID : 4xj4.1

Crystal structure of Vibrio cholerae DncV 3'-deoxy ATP bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: K.29, F.115, D.118, T.119, L.120, R.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.115, A:L.120, A:L.120, A:R.261 Water bridges: A:K.29, A:R.261 EDO.2: 4 residues within 4Å: Chain A: A.269, N.371, M.372, G.375 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.270, A:Q.270, A:N.376 EDO.3: 7 residues within 4Å: Chain A: F.7, Y.11, G.300, M.303, L.354, E.358, I.370 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.11, A:E.358 EDO.4: 7 residues within 4Å: Chain A: M.3, T.4, W.5, E.358, S.359, A.360, L.386 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.358 EDO.5: 5 residues within 4Å: Chain A: P.311, S.312, A.315, M.344, E.348 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.348

2 x 3AT: 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

3AT.6: 15 residues within 4Å: Chain A: Q.112, G.113, S.114, Y.117, L.120, D.131, D.133, V.241, K.264, R.267, S.278, I.279, L.329 Ligands: 3AT.7, MG.8 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.114, A:S.114, A:R.267, A:S.278 Water bridges: A:G.113, A:F.115, A:T.119, A:T.119, A:E.129, A:D.131, A:D.131, A:P.238, A:K.264, A:K.264, A:S.278, A:S.278, A:S.278, A:P.328 Salt bridges: A:K.264, A:K.264 3AT.7: 10 residues within 4Å: Chain A: Q.112, D.133, K.177, T.179, R.182, P.195, Y.197, L.224, S.236 Ligands: 3AT.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.133, A:S.236, A:S.236 Salt bridges: A:K.177, A:R.182

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain A: S.114, D.131, D.133 Ligands: 3AT.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:D.133, H2O.4

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

Cyclic AMP-GMP synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cyclic AMP-GMP synthase

Related Entries With Identical Sequence