SMTL ID : 1x1t.1

Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi Complexed with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: D.38 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.38, A:D.38, H2O.1, H2O.2 MG.4: 1 residues within 4Å: Chain B: D.38 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.38, B:D.38, H2O.308, H2O.309 MG.7: 1 residues within 4Å: Chain C: D.38 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.38, C:D.38, H2O.615, H2O.616 MG.10: 1 residues within 4Å: Chain D: D.38 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.38, D:D.38, H2O.922, H2O.923

4 x CAC: CACODYLATE ION(Non-covalent)

CAC.2: 8 residues within 4Å: Chain A: Q.94, S.142, H.144, K.152, Y.155, W.187, W.257 Ligands: NAD.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.142, A:K.152, A:Y.155 Water bridges: A:K.152 CAC.5: 8 residues within 4Å: Chain B: Q.94, S.142, H.144, K.152, Y.155, W.187, W.257 Ligands: NAD.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.142, B:K.152, B:Y.155 Water bridges: B:K.152 CAC.8: 8 residues within 4Å: Chain C: Q.94, S.142, H.144, K.152, Y.155, W.187, W.257 Ligands: NAD.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.142, C:H.144, C:K.152, C:Y.155, C:Y.155 Water bridges: C:K.152 CAC.11: 8 residues within 4Å: Chain D: Q.94, S.142, H.144, K.152, Y.155, W.187, W.257 Ligands: NAD.12 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.142, D:H.144, D:K.152, D:Y.155, D:Y.155 Water bridges: D:K.152

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

NAD.3: 27 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, L.113, I.140, A.141, S.142, Y.155, K.159, P.185, G.186, W.187, V.188, T.190 Ligands: CAC.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.16, A:P.185 Hydrogen bonds: A:T.13, A:T.13, A:S.14, 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:G.92, A:Y.155, A:K.159, A:V.188, A:V.188 Water bridges: A:G.17, A:G.35, A:S.65, A:N.90 pi-Stacking: A:F.36 NAD.6: 27 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 Ligands: CAC.5 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:I.16, B:P.185 Hydrogen bonds: B:T.13, B:T.13, B:S.14, 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:G.92, B:Y.155, B:K.159, B:V.188, B:V.188 Water bridges: B:G.17, B:G.35, B:S.65, B:N.90 pi-Stacking: B:F.36 NAD.9: 27 residues within 4Å: Chain C: 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 Ligands: CAC.8 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:I.16, C:P.185 Hydrogen bonds: C:T.13, C:T.13, C:S.14, 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:G.92, C:K.159, C:V.188, C:V.188, C:T.190 Water bridges: C:G.17, C:G.35, C:S.65, C:N.90 pi-Stacking: C:F.36 NAD.12: 27 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, 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 Ligands: CAC.11 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:I.16, D:P.185 Hydrogen bonds: D:T.13, 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:G.92, D:K.159, D:V.188, D:V.188, D:T.190 Water bridges: D:G.17, D:G.35, D:S.65, D:N.90 pi-Stacking: D:F.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ito, K. et al., d-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi: Molecular Cloning of the Enzyme Gene and Crystal Structure of the Enzyme. J.Mol.Biol. (2006)

Release Date

2006-01-10

Peptides

D(-)-3-hydroxybutyrate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

D(-)-3-hydroxybutyrate dehydrogenase

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