SMTL ID : 1f8f.1

CRYSTAL STRUCTURE OF BENZYL ALCOHOL DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.44, T.46, H.65, C.173 Ligands: NAD.5, EOH.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.44, A:H.65, A:C.173, EOH.6 ZN.2: 5 residues within 4Å: Chain A: C.94, G.95, C.97, C.100, C.108 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.94, A:C.97, A:C.100, A:C.108 ZN.7: 6 residues within 4Å: Chain B: C.44, T.46, H.65, C.173 Ligands: NAD.11, EOH.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:C.44, B:H.65, B:C.173, EOH.12 ZN.8: 5 residues within 4Å: Chain B: C.94, G.95, C.97, C.100, C.108 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.94, B:C.97, B:C.100, B:C.108 ZN.13: 6 residues within 4Å: Chain C: C.44, T.46, H.65, C.173 Ligands: NAD.17, EOH.18 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.44, C:H.65, C:C.173 ZN.14: 5 residues within 4Å: Chain C: C.94, G.95, C.97, C.100, C.108 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.94, C:C.97, C:C.100, C:C.108 ZN.19: 6 residues within 4Å: Chain D: C.44, T.46, H.65, C.173 Ligands: NAD.23, EOH.24 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:C.44, D:H.65, D:C.173, EOH.24 ZN.20: 5 residues within 4Å: Chain D: C.94, G.95, C.97, C.100, C.108 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.94, D:C.97, D:C.100, D:C.108

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: R.114, S.121, R.152 Chain B: T.79 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.121, A:S.121 Water bridges: A:R.114, A:S.121, A:R.152 Salt bridges: A:R.114, A:R.152 SO4.4: 3 residues within 4Å: Chain A: K.323, E.327, R.330 8 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:E.327, A:E.327 Water bridges: A:K.323, C:N.260, C:N.260, B:T.98 Salt bridges: A:K.323, A:R.330 SO4.9: 4 residues within 4Å: Chain A: T.79 Chain B: R.114, S.121, R.152 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.121, B:S.121 Water bridges: B:R.114, B:S.121, B:R.152 Salt bridges: B:R.114, B:R.152 SO4.10: 3 residues within 4Å: Chain B: K.323, E.327, R.330 8 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:E.327, B:E.327 Water bridges: B:K.323, A:T.98, D:N.260, D:N.260 Salt bridges: B:K.323, B:R.330 SO4.15: 4 residues within 4Å: Chain C: R.114, S.121, R.152 Chain D: T.79 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.121, C:S.121 Water bridges: C:R.114, C:S.121, C:R.152 Salt bridges: C:R.114, C:R.152 SO4.16: 3 residues within 4Å: Chain C: K.323, E.327, R.330 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:E.327 Water bridges: C:K.323, A:N.260, A:N.260 Salt bridges: C:K.323, C:R.330 SO4.21: 4 residues within 4Å: Chain C: T.79 Chain D: R.114, S.121, R.152 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.121, D:S.121 Water bridges: D:R.114, D:S.121, D:R.152 Salt bridges: D:R.114, D:R.152 SO4.22: 3 residues within 4Å: Chain D: K.323, E.327, R.330 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Water bridges: B:N.260, B:N.260, D:K.323 Hydrogen bonds: D:E.327 Salt bridges: D:K.323, D:R.330

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

NAD.5: 24 residues within 4Å: Chain A: H.45, T.46, C.173, T.177, A.199, G.200, A.201, V.202, D.222, I.223, V.224, R.227, S.242, S.265, T.266, V.288, G.289, A.290, V.314, V.315, E.316 Chain D: L.305 Ligands: ZN.1, EOH.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:H.45, A:T.177, A:A.201, A:V.202, A:I.223, A:R.227, A:S.242, A:V.288, A:A.290, A:E.316 Water bridges: A:G.200, A:G.203, A:S.358, A:L.364, A:K.365 Salt bridges: A:R.227 NAD.11: 24 residues within 4Å: Chain B: H.45, T.46, C.173, T.177, A.199, G.200, A.201, V.202, D.222, I.223, V.224, R.227, S.242, S.265, T.266, V.288, G.289, A.290, V.314, V.315, E.316 Chain C: L.305 Ligands: ZN.7, EOH.12 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:H.45, B:T.177, B:A.201, B:V.202, B:I.223, B:R.227, B:S.242, B:V.288, B:A.290, B:E.316 Water bridges: B:G.200, B:G.203, B:S.358, B:L.364, B:K.365 Salt bridges: B:R.227 NAD.17: 24 residues within 4Å: Chain B: L.305 Chain C: H.45, T.46, C.173, T.177, A.199, G.200, A.201, V.202, D.222, I.223, V.224, R.227, S.242, S.265, T.266, V.288, G.289, A.290, V.314, V.315, E.316 Ligands: ZN.13, EOH.18 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:H.45, C:A.201, C:V.202, C:I.223, C:R.227, C:S.242, C:V.288, C:A.290, C:E.316 Water bridges: C:G.200, C:G.203, C:S.358, C:L.364, C:K.365 Salt bridges: C:R.227 NAD.23: 24 residues within 4Å: Chain A: L.305 Chain D: H.45, T.46, C.173, T.177, A.199, G.200, A.201, V.202, D.222, I.223, V.224, R.227, S.242, S.265, T.266, V.288, G.289, A.290, V.314, V.315, E.316 Ligands: ZN.19, EOH.24 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:H.45, D:A.201, D:V.202, D:I.223, D:R.227, D:S.242, D:V.288, D:A.290, D:E.316 Water bridges: D:G.200, D:G.203, D:S.358, D:L.364, D:K.365 Salt bridges: D:R.227

4 x EOH: ETHANOL(Non-functional Binders)

EOH.6: 8 residues within 4Å: Chain A: C.44, T.46, H.65, F.140, C.173, E.316 Ligands: ZN.1, NAD.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.140 EOH.12: 8 residues within 4Å: Chain B: C.44, T.46, H.65, F.140, C.173, E.316 Ligands: ZN.7, NAD.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.140 EOH.18: 8 residues within 4Å: Chain C: C.44, T.46, H.65, F.140, C.173, E.316 Ligands: ZN.13, NAD.17 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.140 Hydrogen bonds: C:T.46, C:H.65 EOH.24: 8 residues within 4Å: Chain D: C.44, T.46, H.65, F.140, C.173, E.316 Ligands: ZN.19, NAD.23 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.140 Hydrogen bonds: D:T.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beauchamp, J.C. et al., Crystal Structure of Benzyl Alcohol Dehydrogenase from Acinetobacter calcoaceticus. To be Published

Release Date

2003-07-08

Peptides

BENZYL ALCOHOL DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

BENZYL ALCOHOL DEHYDROGENASE