SMTL ID : 4u0m.1 (1 other biounit)

Structure of the Vibrio cholerae di-nucleotide cyclase (DncV) mutant D193N in complex with ATP, GTP and 5MTHFGLU2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

GTP.1: 16 residues within 4Å: Chain A: Q.112, G.113, S.114, Y.117, L.120, D.131, D.133, V.264, K.287, R.290, S.301, D.345, D.348, L.352 Ligands: ATP.2, MG.3 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.113, A:S.114, A:S.114, A:S.114, A:Y.117, A:Y.117, A:D.131, A:R.290, A:S.301, A:D.345, A:D.345 Water bridges: A:F.115, A:F.115, A:T.119, A:T.119, A:P.261, A:E.265, A:K.287, A:S.301, A:S.301, A:I.302, A:D.348 Salt bridges: A:K.287, A:K.287, A:D.348

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 9 residues within 4Å: Chain A: Q.112, D.133, K.177, T.179, R.182, N.193, L.247, S.259 Ligands: GTP.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.133, A:D.133, A:T.179, A:N.193, A:S.259 Water bridges: A:Y.197 Salt bridges: A:R.182, A:R.182

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: 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.7

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.4: 21 residues within 4Å: Chain A: R.36, R.40, R.44, R.108, F.109, W.110, T.111, Q.116, Y.137, I.199, F.204, Q.208, Y.238, E.239, L.240, D.241, S.242, V.245, D.260, P.261, K.262 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:R.108, A:W.110, A:F.204 Hydrogen bonds: A:R.40, A:R.40, A:R.108, A:F.109, A:F.109, A:T.111, A:Q.116, A:Y.137, A:Y.238, A:L.240, A:K.262 Water bridges: A:E.239, A:S.242 Salt bridges: A:R.36, A:R.36, A:R.40, A:R.44, A:R.108, A:D.260 pi-Stacking: A:W.110

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
A

Cyclic AMP-GMP synthase

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