SMTL ID : 4xj5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.131, D.133 Ligands: MG.2, GH3.14 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:D.133, H2O.7 MG.2: 6 residues within 4Å: Chain A: D.131, D.133, D.193 Ligands: MG.1, GH3.13, GH3.14 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:D.131, A:D.133, A:D.193, H2O.8

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

EDO.3: 5 residues within 4Å: Chain A: A.269, Q.270, N.371, M.372, G.375 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.376 EDO.4: 5 residues within 4Å: Chain A: R.267, G.274, G.275, P.276, S.277 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.275 Water bridges: A:R.267, A:R.267, A:G.274, A:G.274 EDO.5: 3 residues within 4Å: Chain A: A.293, D.295, E.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.301 Water bridges: A:D.295 EDO.6: 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.7: 4 residues within 4Å: Chain A: Q.270, W.271, D.272, V.273 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.272, A:V.273 Water bridges: A:Q.125, A:Q.125, A:Q.270 EDO.8: 8 residues within 4Å: Chain A: L.24, K.29, S.114, F.115, D.118, T.119, L.120, R.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.118, A:D.118, A:L.120, A:R.261 Water bridges: A:K.29, A:K.29 EDO.9: 4 residues within 4Å: Chain A: R.108, F.109, W.110, Y.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.108, A:R.108 EDO.10: 4 residues within 4Å: Chain A: I.288, S.291, H.309, E.313 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain A: F.7, Y.11, G.300, E.301, M.303, L.354, I.370 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.11, A:Y.11 Water bridges: A:F.7 EDO.12: 4 residues within 4Å: Chain A: H.255, H.294, D.295, A.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.296 Water bridges: A:H.294, A:H.294, A:D.295

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

GH3.13: 13 residues within 4Å: Chain A: Q.112, D.133, K.177, T.179, C.180, D.193, P.195, Y.197, L.224, S.236, P.238 Ligands: MG.2, GH3.14 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.112, A:D.133, A:D.133, A:T.179, A:R.182, A:Y.197, A:Y.197, A:S.236, A:S.236 Salt bridges: A:K.177 GH3.14: 19 residues within 4Å: Chain A: Q.112, G.113, S.114, Y.117, L.120, D.131, D.133, S.236, P.238, V.241, K.264, S.278, I.279, D.322, D.325, L.329 Ligands: MG.1, MG.2, GH3.13 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:Q.112, A:S.114, A:S.114, A:S.114, A:Y.117, A:P.238, A:R.267, A:S.278, A:D.322, A:D.322 Water bridges: A:F.115, A:F.115, A:T.119, A:D.131, A:K.264, A:S.278, A:S.278, A:D.325 Salt bridges: A:K.264, A:K.264, A:D.325

1 x NA: SODIUM ION(Non-functional Binders)

NA.15: 5 residues within 4Å: Chain A: W.266, Q.270, K.346, L.350, I.353 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.346

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

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