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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: G.18, A.20, S.21, G.22, I.23, D.42, I.43, M.67, D.68, V.69, N.95, A.96, G.97, I.98, I.118, H.119, M.146, G.147, S.148, Y.161, K.165, P.191, G.192, F.193, V.194, T.196, P.197, L.198, V.199 Ligands: QT8.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.191 Hydrogen bonds: A:G.18, A:A.20, A:S.21, A:I.23, A:I.43, A:D.68, A:V.69, A:N.95, A:G.97, A:K.165, A:V.194, A:V.194, A:T.196, A:T.196, A:L.198 Water bridges: A:S.21, A:G.24, A:N.95 NAD.3: 30 residues within 4Å: Chain B: G.18, A.20, S.21, G.22, I.23, D.42, I.43, M.67, D.68, V.69, N.95, A.96, G.97, I.98, I.118, H.119, M.146, G.147, S.148, Y.161, K.165, P.191, G.192, F.193, V.194, T.196, P.197, L.198, V.199 Ligands: QT8.4 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.23, B:P.191 Hydrogen bonds: B:G.18, B:S.21, B:I.23, B:I.43, B:D.68, B:D.68, B:V.69, B:N.95, B:G.97, B:Y.161, B:K.165, B:V.194, B:V.194, B:L.198 Water bridges: B:S.21, B:S.21, B:G.24, B:N.44, B:N.95, B:H.119 NAD.5: 30 residues within 4Å: Chain C: G.18, A.20, S.21, G.22, I.23, D.42, I.43, M.67, D.68, V.69, N.95, A.96, G.97, I.98, I.118, H.119, M.146, G.147, S.148, Y.161, K.165, P.191, G.192, F.193, V.194, T.196, P.197, L.198, V.199 Ligands: QT8.6 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:P.191 Hydrogen bonds: C:G.18, C:A.20, C:S.21, C:I.23, C:I.43, C:D.68, C:V.69, C:N.95, C:G.97, C:K.165, C:V.194, C:V.194, C:T.196, C:T.196, C:L.198 Water bridges: C:S.21, C:G.24, C:N.95 NAD.7: 30 residues within 4Å: Chain D: G.18, A.20, S.21, G.22, I.23, D.42, I.43, M.67, D.68, V.69, N.95, A.96, G.97, I.98, I.118, H.119, M.146, G.147, S.148, Y.161, K.165, P.191, G.192, F.193, V.194, T.196, P.197, L.198, V.199 Ligands: QT8.8 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:I.23, D:P.191 Hydrogen bonds: D:G.18, D:S.21, D:I.23, D:I.43, D:D.68, D:D.68, D:V.69, D:N.95, D:G.97, D:Y.161, D:K.165, D:V.194, D:V.194, D:L.198 Water bridges: D:S.21, D:S.21, D:G.24, D:N.44, D:N.95, D:H.119

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

QT8.2: 10 residues within 4Å: Chain A: Q.99, S.148, H.150, K.158, Y.161, F.193, L.198, V.199, Q.202 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.161, A:F.193, A:L.198, A:V.199 Hydrogen bonds: A:Q.99, A:Q.202 Salt bridges: A:H.150, A:K.158 QT8.4: 9 residues within 4Å: Chain B: Q.99, S.148, H.150, K.158, Y.161, F.193, V.199, Q.202 Ligands: NAD.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.161, B:F.193, B:V.199 Hydrogen bonds: B:Q.99, B:Q.202 Salt bridges: B:H.150, B:K.158 QT8.6: 10 residues within 4Å: Chain C: Q.99, S.148, H.150, K.158, Y.161, F.193, L.198, V.199, Q.202 Ligands: NAD.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.161, C:F.193, C:L.198, C:V.199 Hydrogen bonds: C:Q.99, C:Q.202 Salt bridges: C:H.150, C:K.158 QT8.8: 9 residues within 4Å: Chain D: Q.99, S.148, H.150, K.158, Y.161, F.193, V.199, Q.202 Ligands: NAD.7 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.161, D:F.193, D:V.199 Hydrogen bonds: D:Q.99, D:Q.202 Salt bridges: D:H.150, D:K.158

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

Putative beta-hydroxybutyrate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Putative beta-hydroxybutyrate dehydrogenase

Related Entries With Identical Sequence