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

Crystal structure of gamma-hydroxybutyrate dehydrogenase from Geobacter metallireducens in complex with NADP+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 26 residues within 4Å: Chain A: G.8, L.9, G.10, I.11, M.12, N.31, R.32, S.33, K.36, M.64, L.65, A.66, A.70, E.73, V.74, T.96, V.121, G.123, S.124, K.125, K.171, A.231, F.232, P.233, H.236, K.239 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:V.121, A:F.232 Hydrogen bonds: A:L.9, A:I.11, A:M.12, A:N.31, A:N.31, A:S.33, A:L.65, A:A.66, A:E.73, A:T.96, A:T.96, A:K.125, A:A.231, A:K.239, A:K.239 Water bridges: A:G.10, A:G.13, A:R.32, A:R.32, A:R.32, A:R.32, A:S.33, A:S.33, A:K.36 Salt bridges: A:R.32, A:K.36, A:H.236, A:H.236 pi-Cation interactions: A:R.32, A:R.32 NAP.5: 27 residues within 4Å: Chain B: G.8, L.9, G.10, I.11, M.12, N.31, R.32, S.33, K.36, M.64, L.65, A.66, A.70, E.73, V.74, S.95, T.96, V.121, G.123, S.124, K.125, K.171, A.231, F.232, P.233, H.236, K.239 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:F.232 Hydrogen bonds: B:L.9, B:I.11, B:M.12, B:G.13, B:N.31, B:N.31, B:S.33, B:S.33, B:L.65, B:A.66, B:E.73, B:T.96, B:T.96, B:K.125, B:A.231, B:K.239, B:K.239 Water bridges: B:R.32, B:R.32 Salt bridges: B:R.32, B:K.36, B:H.236, B:H.236 pi-Cation interactions: B:R.32, B:R.32 NAP.6: 26 residues within 4Å: Chain C: G.8, L.9, G.10, I.11, M.12, W.30, N.31, R.32, S.33, M.64, L.65, A.66, A.70, E.73, V.74, T.96, V.121, G.123, S.124, K.125, K.171, A.231, F.232, P.233, H.236, K.239 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:V.121, C:F.232 Hydrogen bonds: C:L.9, C:I.11, C:M.12, C:N.31, C:N.31, C:R.32, C:S.33, C:S.33, C:L.65, C:A.66, C:E.73, C:T.96, C:T.96, C:K.125, C:A.231, C:K.239, C:K.239 Water bridges: C:G.10, C:G.13, C:R.32, C:K.235 Salt bridges: C:R.32, C:H.236, C:H.236 pi-Cation interactions: C:R.32, C:R.32 NAP.8: 26 residues within 4Å: Chain D: G.8, L.9, G.10, I.11, M.12, N.31, R.32, S.33, K.36, M.64, L.65, A.66, A.70, E.73, V.74, S.95, T.96, V.121, G.123, S.124, K.171, A.231, F.232, P.233, H.236, K.239 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:F.232 Hydrogen bonds: D:L.9, D:G.10, D:I.11, D:M.12, D:N.31, D:N.31, D:S.33, D:S.33, D:L.65, D:A.66, D:E.73, D:T.96, D:T.96, D:K.125, D:A.231, D:K.239, D:K.239 Water bridges: D:G.13, D:K.36 Salt bridges: D:R.32, D:K.36, D:H.236, D:H.236 pi-Cation interactions: D:R.32, D:R.32

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: R.32, S.33, P.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.33 Water bridges: A:R.32 GOL.3: 6 residues within 4Å: Chain A: L.203, G.207, A.212, N.213, F.216, A.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.213

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: A.246, D.249 Chain D: R.242 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.249 PEG.7: 7 residues within 4Å: Chain C: L.203, I.206, G.207, A.212, N.213, F.216, A.217 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.213 Water bridges: C:G.207 PEG.9: 7 residues within 4Å: Chain D: L.203, I.206, G.207, A.212, N.213, F.216, A.217 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Structural characterization of a beta-hydroxyacid dehydrogenase from Geobacter sulfurreducens and Geobacter metallireducens with succinic semialdehyde reductase activity. Biochimie (2014)

Release Date

2011-12-07

Peptides

6-phosphogluconate dehydrogenase, NAD-binding: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

6-phosphogluconate dehydrogenase, NAD-binding

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