SMTL ID : 3vdq.1

Crystal structure of alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase in complex with NAD(+) and acetate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 8 residues within 4Å: Chain A: Q.94, H.144, K.152, W.187, L.192, V.193, Q.196 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.187, A:L.192, A:V.193 Hydrogen bonds: A:Q.94, A:Q.196 Water bridges: A:H.144 Salt bridges: A:H.144, A:K.152 ACT.4: 8 residues within 4Å: Chain B: Q.94, H.144, K.152, Y.155, W.187, L.192, Q.196 Ligands: NAD.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.187, B:L.192 Hydrogen bonds: B:Q.94, B:Q.196 Water bridges: B:H.144 Salt bridges: B:H.144, B:K.152 ACT.9: 9 residues within 4Å: Chain C: Q.94, H.144, K.152, Y.155, W.187, L.192, V.193, Q.196 Ligands: NAD.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.187, C:L.192, C:V.193 Hydrogen bonds: C:Q.94, C:Q.196 Water bridges: C:H.144 Salt bridges: C:H.144, C:K.152 ACT.12: 8 residues within 4Å: Chain D: Q.94, H.144, K.152, Y.155, W.187, L.192, Q.196 Ligands: NAD.14 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.187, D:L.192 Hydrogen bonds: D:Q.94, D:Q.196 Water bridges: D:H.144 Salt bridges: D:H.144, D:K.152

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: S.149, V.150, K.219 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: S.149, V.150, K.219 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain C: S.149, V.150, K.219 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain D: S.149, V.150, K.219 Ligand excluded by PLIP

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

NAD.3: 29 residues within 4Å: Chain A: G.11, T.13, S.14, G.15, I.16, N.34, F.36, A.62, D.63, L.64, S.65, N.90, A.91, G.92, L.113, I.140, A.141, S.142, Y.155, K.159, P.185, G.186, W.187, V.188, T.190, P.191, L.192, V.193 Ligands: ACT.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.185 Hydrogen bonds: A:G.11, A:T.13, A:T.13, A:S.14, A:S.14, A:I.16, A:F.36, A:D.63, A:L.64, A:S.65, A:N.90, A:K.159, A:V.188, A:V.188, A:T.190 Water bridges: A:N.90 pi-Stacking: A:F.36, A:F.36 NAD.6: 28 residues within 4Å: Chain B: G.11, T.13, S.14, G.15, I.16, N.34, F.36, A.62, D.63, L.64, N.90, A.91, G.92, L.113, I.140, A.141, S.142, Y.155, K.159, P.185, G.186, W.187, V.188, T.190, P.191, L.192, V.193 Ligands: ACT.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:P.185 Hydrogen bonds: B:G.11, B:T.13, B:S.14, B:S.14, B:I.16, B:F.36, B:D.63, B:L.64, B:N.90, B:Y.155, B:K.159, B:V.188, B:V.188 Water bridges: B:T.13, B:S.14, B:S.14, B:S.14, B:S.14, B:G.17, B:N.90 NAD.11: 28 residues within 4Å: Chain C: G.11, T.13, S.14, G.15, I.16, N.34, F.36, A.62, D.63, L.64, N.90, A.91, G.92, L.113, I.140, A.141, S.142, Y.155, K.159, P.185, G.186, W.187, V.188, T.190, P.191, L.192, V.193 Ligands: ACT.9 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:P.185 Hydrogen bonds: C:G.11, C:T.13, C:T.13, C:S.14, C:S.14, C:I.16, C:F.36, C:D.63, C:D.63, C:L.64, C:N.90, C:Y.155, C:K.159, C:V.188, C:V.188 Water bridges: C:T.13, C:S.14, C:S.14, C:G.17, C:F.36, C:N.90 NAD.14: 29 residues within 4Å: Chain D: G.11, T.13, S.14, G.15, I.16, N.34, G.35, F.36, A.62, D.63, L.64, N.90, A.91, G.92, L.113, I.140, A.141, S.142, Y.155, K.159, P.185, G.186, W.187, V.188, T.190, P.191, L.192, V.193 Ligands: ACT.12 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:P.185 Hydrogen bonds: D:G.11, D:T.13, D:S.14, D:S.14, D:I.16, D:F.36, D:D.63, D:L.64, D:N.90, D:K.159, D:V.188, D:V.188, D:T.190, D:T.190 Water bridges: D:S.14, D:S.14, D:S.14, D:G.17, D:N.90

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain B: V.147, R.260 Chain D: V.147, R.260 No protein-ligand interaction detected (PLIP) CA.8: 4 residues within 4Å: Chain A: V.147, R.260 Chain C: V.147, R.260 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoque, M.M. et al., The structures of Alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase before and after NAD+ and acetate binding suggest a dynamical reaction mechanism as a member of the SDR family. Acta Crystallogr.,Sect.D (2008)

Release Date

2012-02-29

Peptides

D-3-hydroxybutyrate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

D-3-hydroxybutyrate dehydrogenase

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