SMTL ID : 3o03.2 (1 other biounit)

Quaternary complex structure of gluconate 5-dehydrogenase from streptococcus suis type 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: S.170, M.171, M.172, P.213, G.214 Ligands: NAP.2, GCO.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.213, H2O.8 CA.4: 7 residues within 4Å: Chain B: S.170, M.171, M.172, P.213, G.214 Ligands: NAP.5, GCO.6 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:P.213, H2O.16

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 26 residues within 4Å: Chain A: G.41, S.43, Y.44, G.45, I.46, N.64, D.65, I.66, L.70, C.90, D.91, V.92, N.118, A.119, G.120, I.121, I.141, I.168, C.169, Y.183, K.187, P.213, I.216, T.218 Ligands: CA.1, GCO.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.46, A:P.213 Hydrogen bonds: A:G.41, A:Y.44, A:I.46, A:D.91, A:D.91, A:V.92, A:N.118, A:G.120, A:G.120, A:K.187, A:I.216 Water bridges: A:S.43, A:G.47, A:N.118, A:I.121, A:I.216 NAP.5: 26 residues within 4Å: Chain B: G.41, S.43, Y.44, G.45, I.46, N.64, D.65, I.66, L.70, C.90, D.91, V.92, N.118, A.119, G.120, I.121, I.141, I.168, C.169, Y.183, K.187, P.213, I.216, T.218 Ligands: CA.4, GCO.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.46, B:P.213 Hydrogen bonds: B:G.41, B:Y.44, B:I.46, B:D.91, B:D.91, B:V.92, B:N.118, B:G.120, B:G.120, B:K.187, B:I.216 Water bridges: B:S.43, B:G.47, B:N.118, B:I.121, B:I.216

2 x GCO: D-gluconic acid(Non-covalent)

GCO.3: 9 residues within 4Å: Chain A: I.122, R.124, S.170, M.172, R.177, V.180, Y.183 Ligands: CA.1, NAP.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.177, A:Y.183 Water bridges: A:R.124 Salt bridges: A:R.124, A:R.177 GCO.6: 9 residues within 4Å: Chain B: I.122, R.124, S.170, M.172, R.177, V.180, Y.183 Ligands: CA.4, NAP.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.177, B:Y.183 Water bridges: B:R.124 Salt bridges: B:R.124, B:R.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Q. et al., Structural Insight Into the Catalytic Mechanism of Gluconate 5-Dehydrogenase from Streptococcus Suis: Crystal Structures of the Substrate-Free and Quaternary Complex Enzymes. Protein Sci. (2009)

Release Date

2010-12-15

Peptides

Dehydrogenase with different specificities: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dehydrogenase with different specificities

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