SMTL ID : 2ztl.1

Closed conformation of D-3-hydroxybutyrate dehydrogenase complexed with NAD+ and L-3-hydroxybutyrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: 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, P.191, L.192, V.193 Ligands: 3HL.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.16, 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:L.64, A:S.65, A:N.90, A:G.92, A:K.159, A:V.188, A:V.188 Water bridges: A:S.14, A:G.17, A:G.35, A:N.90 NAD.4: 30 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, P.191, L.192, V.193 Ligands: 3HL.5 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.16, 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:D.63, B:L.64, B:S.65, B:N.90, B:Y.155, B:K.159, B:V.188, B:V.188, B:T.190 Water bridges: B:G.17, B:N.90 pi-Stacking: B:F.36, B:F.36 NAD.7: 31 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, 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: 3HL.8 21 PLIP interactions: 21 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:L.64, C:S.65, C:N.90, C:K.159, C:V.188, C:V.188, C:T.190 Water bridges: C:S.14, C:G.17, C:G.35, C:N.90 NAD.9: 31 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, P.191, L.192, V.193 Ligands: 3HL.10 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:I.16, D:P.185 Hydrogen bonds: D:G.11, D:T.13, D:T.13, 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:Y.155, D:K.159, D:V.188, D:V.188, D:T.190 Water bridges: D:S.14, D:S.14, D:G.17, D:S.65, D:N.90

4 x 3HL: (3S)-3-HYDROXYBUTANOIC ACID(Non-covalent)

3HL.2: 10 residues within 4Å: Chain A: Q.94, S.142, H.144, K.152, Y.155, W.187, L.192, Q.196, W.257 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.187, A:L.192, A:W.257 Hydrogen bonds: A:Q.94, A:Y.155, A:Y.155, A:Q.196 Salt bridges: A:H.144, A:K.152 3HL.5: 10 residues within 4Å: Chain B: Q.94, S.142, H.144, K.152, Y.155, W.187, L.192, Q.196, W.257 Ligands: NAD.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.155, B:W.187, B:L.192, B:W.257 Hydrogen bonds: B:Q.94, B:S.142, B:Y.155, B:Q.196 Salt bridges: B:H.144, B:K.152 3HL.8: 10 residues within 4Å: Chain C: Q.94, S.142, H.144, K.152, Y.155, W.187, L.192, Q.196, W.257 Ligands: NAD.7 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.187, C:W.187, C:L.192, C:W.257 Hydrogen bonds: C:Q.94, C:Y.155, C:Y.155, C:Q.196 Salt bridges: C:H.144, C:K.152 3HL.10: 10 residues within 4Å: Chain D: Q.94, S.142, H.144, K.152, Y.155, W.187, L.192, Q.196, W.257 Ligands: NAD.9 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.187, D:W.187, D:L.192, D:W.257 Hydrogen bonds: D:Q.94, D:Y.155, D:Q.196 Salt bridges: D:H.144, D:K.152

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: R.260 Chain D: R.260 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: R.260 Chain C: R.260 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 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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