SMTL ID : 4ty0.1 (1 other biounit)

Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase in complex with linear intermediate 5' pppA(3',5')pG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.131, D.133, H.191, D.193 Ligands: MG.2, 38V.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.133, A:D.193, H2O.3, H2O.4 MG.2: 4 residues within 4Å: Chain A: D.131, D.133 Ligands: MG.1, 38V.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:D.133, H2O.4

1 x 38V: [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3-[[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid(Non-covalent)

38V.3: 21 residues within 4Å: Chain A: Q.112, G.113, S.114, Y.117, D.131, D.133, K.177, T.179, C.180, D.193, P.195, Y.197, L.247, S.259, P.261, V.264, K.287, S.301, L.352 Ligands: MG.1, MG.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:Q.112, A:S.114, A:S.114, A:S.114, A:Y.117, A:T.179, A:Y.197, A:Y.197, A:Y.197, A:S.259, A:S.259, A:R.290, A:S.301 Water bridges: A:G.113, A:F.115, A:F.115, A:D.131, A:D.131, A:D.133, A:K.287, A:K.287 Salt bridges: A:K.177, A:K.287

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: F.109, W.110, Y.137, F.204, K.262 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.204 Salt bridges: A:K.262 ACT.5: 1 residues within 4Å: Chain A: F.124 No protein-ligand interaction detected (PLIP) ACT.6: 2 residues within 4Å: Chain A: E.342, S.346 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kranzusch, P.J. et al., Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity. Cell (2014)

Release Date

2014-08-13

Peptides

Cyclic AMP-GMP synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cyclic AMP-GMP synthase

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