SMTL ID : 2vwg.1

Haloferax mediterranei glucose dehydrogenase in complex with NADP, Zn and gluconolactone.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 27 residues within 4Å: Chain A: D.38, G.39, T.40, I.154, G.180, N.181, G.182, S.183, L.184, L.205, G.206, R.207, R.208, S.228, A.249, T.250, G.251, F.252, H.255, L.272, G.273, V.274, S.301, V.302, N.303 Chain B: V.292 Ligands: LGC.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.154, A:L.184 Hydrogen bonds: A:G.39, A:N.181, A:S.183, A:S.183, A:L.184, A:R.207, A:R.208, A:S.228, A:L.272, A:V.274, A:N.303 Water bridges: A:N.181, A:G.182, A:G.185, A:R.207, A:S.228, A:S.228, A:H.255 Salt bridges: A:R.207, A:R.208 pi-Cation interactions: A:R.207 NAP.4: 27 residues within 4Å: Chain A: V.292 Chain B: D.38, G.39, T.40, I.154, G.180, N.181, G.182, S.183, L.184, L.205, G.206, R.207, R.208, S.228, A.249, T.250, G.251, F.252, H.255, L.272, G.273, V.274, S.301, V.302, N.303 Ligands: LGC.5 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.154, B:L.184 Hydrogen bonds: B:G.39, B:N.181, B:S.183, B:S.183, B:L.184, B:R.207, B:R.208, B:S.228, B:L.272, B:V.274, B:N.303 Water bridges: B:N.181, B:G.182, B:G.185, B:R.207, B:S.228, B:S.228, B:H.255 Salt bridges: B:R.207, B:R.208 pi-Cation interactions: B:R.207

2 x LGC: D-glucono-1,5-lactone(Non-covalent)

LGC.2: 13 residues within 4Å: Chain A: D.38, T.40, H.49, H.63, V.87, E.114, I.117, E.150, I.154, V.302, N.303 Ligands: NAP.1, ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.40, A:H.49, A:E.150, A:E.150, A:N.303 Salt bridges: A:H.63 LGC.5: 13 residues within 4Å: Chain B: D.38, T.40, H.49, H.63, V.87, E.114, I.117, E.150, I.154, V.302, N.303 Ligands: NAP.4, ZN.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.49, B:E.150, B:E.150, B:E.150, B:N.303 Salt bridges: B:H.63

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: D.38, H.63, E.64, E.150 Ligands: LGC.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.38, A:H.63, A:E.64, H2O.6 ZN.6: 5 residues within 4Å: Chain B: D.38, H.63, E.64, E.150 Ligands: LGC.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.38, B:H.63, B:E.64, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baker, P.J. et al., Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily. Proc. Natl. Acad. Sci. U.S.A. (2009)

Release Date

2009-01-13

Peptides

GLUCOSE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLUCOSE DEHYDROGENASE

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