SMTL ID : 4u03.2 (1 other biounit)

Structure of the vibrio cholerae di-nucleotide cyclase (DncV) in complex with GTP and 5MTHFGLU2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

monomer

Ligands

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

GTP.1: 17 residues within 4Å: Chain A: Q.112, G.113, S.114, Y.117, D.131, D.133, P.261, V.264, K.287, R.290, S.301, I.302, D.345, D.348, L.352 Ligands: GTP.2, MG.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:Q.112, A:G.113, A:S.114, A:S.114, A:Y.117, A:Y.117, A:P.261, A:R.290, A:S.301, A:D.345, A:D.345 Water bridges: A:F.115, A:T.119, A:D.131, A:K.287, A:S.301, A:I.302 Salt bridges: A:K.287, A:K.287, A:D.348 GTP.2: 13 residues within 4Å: Chain A: Q.112, D.131, D.133, K.177, T.179, C.180, R.182, D.193, Y.197, L.247, S.259 Ligands: GTP.1, MG.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.112, A:D.133, A:T.179, A:Y.197, A:Y.197, A:S.259, A:S.259 Salt bridges: A:K.177, A:K.177, A:K.177, A:R.182, A:R.182

2 x MG: MAGNESIUM ION(Non-covalent)

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

1 x TLL: N-[4-({[(6S)-2-amino-5-methyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-glutamic acid(Non-covalent)

TLL.5: 21 residues within 4Å: Chain A: R.36, R.40, R.108, F.109, W.110, T.111, Q.116, Y.137, I.199, F.204, Q.208, T.237, Y.238, E.239, L.240, D.241, S.242, V.245, D.260, P.261, K.262 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:R.108, A:W.110, A:F.204, A:Y.238 Hydrogen bonds: A:R.40, A:R.40, A:F.109, A:F.109, A:T.111, A:Y.137, A:Y.238, A:Y.238, A:Y.238, A:L.240, A:L.240, A:K.262 Salt bridges: A:R.36, A:R.40, A:D.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, D. et al., Structural Biochemistry of a Vibrio cholerae Dinucleotide Cyclase Reveals Cyclase Activity Regulation by Folates. Mol.Cell (2014)

Release Date

2014-09-17

Peptides

Cyclic AMP-GMP synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Cyclic AMP-GMP synthase

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