SMTL ID : 6zzs.1 (1 other biounit)

Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Acinetobacter baumannii complexed with NAD+ and 3-oxovalerate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 25 residues within 4Å: Chain A: G.14, S.17, G.18, I.19, D.38, M.39, C.63, D.64, V.65, T.66, N.91, A.92, G.93, V.114, M.141, A.142, S.143, Y.156, K.160, P.186, G.187, V.189, T.191, V.194 Ligands: QT8.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.186 Hydrogen bonds: A:S.17, A:S.17, A:S.17, A:S.17, A:S.17, A:I.19, A:M.39, A:D.64, A:D.64, A:V.65, A:N.91, A:G.93, A:Y.156, A:K.160, A:V.189, A:T.191 Water bridges: A:S.17, A:D.38, A:N.91 NAD.3: 25 residues within 4Å: Chain B: G.14, S.17, G.18, I.19, D.38, M.39, C.63, D.64, V.65, N.91, A.92, G.93, V.114, M.141, A.142, S.143, Y.156, K.160, P.186, G.187, Y.188, V.189, T.191, V.194 Ligands: QT8.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.17, B:S.17, B:S.17, B:I.19, B:M.39, B:D.64, B:D.64, B:V.65, B:N.91, B:G.93, B:Y.156, B:K.160, B:V.189, B:T.191 Water bridges: B:G.14, B:G.20, B:N.91 NAD.5: 27 residues within 4Å: Chain C: G.14, S.17, G.18, I.19, D.38, M.39, C.63, D.64, V.65, N.91, A.92, G.93, V.114, M.141, A.142, S.143, Y.156, K.160, P.186, G.187, Y.188, V.189, T.191, L.193, V.194 Ligands: QT8.6, QT8.7 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:P.186 Hydrogen bonds: C:G.14, C:S.17, C:S.17, C:I.19, C:M.39, C:D.64, C:V.65, C:N.91, C:G.93, C:K.160, C:V.189, C:T.191, C:T.191 Water bridges: C:G.20, C:G.20, C:F.94 NAD.8: 27 residues within 4Å: Chain D: G.14, S.17, G.18, I.19, D.38, M.39, C.63, D.64, V.65, N.91, A.92, G.93, F.94, V.114, M.141, A.142, S.143, Y.156, K.160, P.186, G.187, Y.188, V.189, T.191, L.193, V.194 Ligands: QT8.9 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.19, D:P.186 Hydrogen bonds: D:S.17, D:S.17, D:I.19, D:M.39, D:D.64, D:V.65, D:N.91, D:G.93, D:G.93, D:K.160, D:V.189, D:T.191, D:T.191 Water bridges: D:G.14, D:G.20, D:F.94

5 x QT8: 3-oxidanylidenepentanoic acid(Non-covalent)

QT8.2: 8 residues within 4Å: Chain A: Q.95, S.143, N.145, K.153, Y.156, L.193, Q.197 Ligands: NAD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.95, A:Y.156, A:Q.197 Salt bridges: A:K.153 QT8.4: 8 residues within 4Å: Chain B: Q.95, S.143, N.145, K.153, Y.156, Y.188, Q.197 Ligands: NAD.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.156, B:Y.188 Hydrogen bonds: B:Q.95, B:Q.197 Water bridges: B:Y.156 Salt bridges: B:K.153 QT8.6: 8 residues within 4Å: Chain C: Q.95, S.143, N.145, K.153, Y.156, L.193, Q.197 Ligands: NAD.5 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.156 Hydrogen bonds: C:Q.95, C:Q.197 Water bridges: C:K.153, C:Y.188 Salt bridges: C:K.153 QT8.7: 5 residues within 4Å: Chain C: M.39, D.64, F.94, K.110 Ligands: NAD.5 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.94, C:F.94 Salt bridges: C:K.110 QT8.9: 8 residues within 4Å: Chain D: Q.95, S.143, N.145, K.153, Y.156, L.193, Q.197 Ligands: NAD.8 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Y.156 Hydrogen bonds: D:Q.95, D:Q.197 Water bridges: D:K.153, D:Q.197 Salt bridges: D:K.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Machado, T.F.G. et al., Dissecting the Mechanism of ( R )-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry. Acs Catalysis (2020)

Release Date

2020-10-07

Peptides

3-hydroxybutyrate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-hydroxybutyrate dehydrogenase

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