SMTL ID : 2ztv.1

The binary complex of D-3-hydroxybutyrate dehydrogenase with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: G.11, T.13, S.14, G.15, I.16, N.34, G.35, F.36, A.62, D.63, L.64, S.65, N.90, A.91, G.92, I.93, 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 22 PLIP interactions: 22 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:F.36, A:D.63, A:D.63, A:L.64, A:S.65, A:N.90, A:Y.155, A:K.159, A:V.188, A:V.188, A:T.190 Water bridges: A:G.17, A:G.35, A:N.90 NAD.3: 26 residues within 4Å: Chain B: G.11, T.13, S.14, G.15, I.16, N.34, G.35, 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 16 PLIP interactions: 16 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:F.36, B:D.63, B:L.64, B:S.65, B:N.90, B:K.159, B:V.188, B:V.188 Water bridges: B:N.90 NAD.5: 26 residues within 4Å: Chain C: G.11, S.12, 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 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:I.16, C:P.185 Hydrogen bonds: C:G.11, C:T.13, C:S.14, C:S.14, C:I.16, C:F.36, C:F.36, C:D.63, C:D.63, C:L.64, C:S.65, C:A.91, C:Y.155, C:K.159, C:V.188, C:T.190 Water bridges: C:G.35, C:N.90 NAD.6: 27 residues within 4Å: Chain D: G.11, S.12, T.13, S.14, G.15, I.16, N.34, G.35, 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 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.16, D:P.185 Hydrogen bonds: D:T.13, D:S.14, D:S.14, D:S.14, D:I.16, D:F.36, D:F.36, D:D.63, D:L.64, D:S.65, D:N.90, D:K.159, D:V.188, D:V.188 Water bridges: D:G.17, D:N.90

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: V.147, R.260 Chain D: V.147, R.260 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: V.147, R.260 Chain C: V.147, R.260 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain D: Y.59, D.60, G.61 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.61 Water bridges: D:G.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakashima, K. et al., Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor. J.Biochem. (2009)

Release Date

2009-08-25

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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