SMTL ID : 4xj3.1

Crystal structure of Vibrio cholerae DncV GTP bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.114, D.131, D.133 Ligands: MG.2, GTP.12 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:D.133, H2O.9 MG.2: 6 residues within 4Å: Chain A: D.131, D.133, D.193 Ligands: MG.1, GTP.12, GTP.13 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.131, H2O.9, H2O.9, H2O.9

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

EDO.3: 4 residues within 4Å: Chain A: K.254, H.255, K.258, A.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.254, A:H.255, A:H.255, A:K.258 EDO.4: 6 residues within 4Å: Chain A: F.124, A.269, Q.270, 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.5: 5 residues within 4Å: Chain A: R.267, G.274, G.275, P.276, S.277 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.275 Water bridges: A:G.274, A:G.274, A:S.278 EDO.6: 6 residues within 4Å: Chain A: W.244, A.283, N.287, E.319, S.320, P.321 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.287, A:E.319 Water bridges: A:W.244, A:E.319 EDO.7: 4 residues within 4Å: Chain A: A.293, H.294, D.295, E.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.301 EDO.8: 5 residues within 4Å: Chain A: P.123, E.129, R.267, D.268 Ligands: GTP.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.267 Water bridges: A:E.129, A:K.264, A:S.278 EDO.9: 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.10: 3 residues within 4Å: Chain A: W.271, D.272, V.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.272, A:V.273, A:V.273 EDO.11: 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:D.118, A:R.261

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.12: 21 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, R.267, S.278, I.279, D.322, D.325, L.329 Ligands: MG.1, MG.2, EDO.8, GTP.13 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:Q.112, A:G.113, A:S.114, A:S.114, A:S.114, A:Y.117, A:Y.117, A:P.238, A:R.267, A:S.278, A:D.322, A:D.322 Water bridges: A:F.115, A:T.119, A:D.131, A:S.236, A:E.242, A:K.264, A:S.278, A:I.279, A:D.325 Salt bridges: A:K.264, A:K.264, A:D.325 GTP.13: 14 residues within 4Å: Chain A: Q.112, D.131, D.133, K.177, T.179, C.180, R.182, D.193, Y.197, L.224, S.236, P.238 Ligands: MG.2, GTP.12 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Q.112, A:D.133, A:T.179, A:D.193, A:Y.197, A:Y.197, A:Y.197, A:S.236 Water bridges: A:R.182, A:R.182, A:R.182 Salt bridges: A:K.177, A:K.177, A:K.177, A:R.182, A:R.182

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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