SMTL ID : 2xaa.1 (2 other biounits)

Alcohol dehydrogenase ADH-'A' from Rhodococcus ruber DSM 44541 at pH 8.5 in complex with NAD and butane-1,4-diol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: H.39, S.40, D.153, T.157, G.179, V.180, G.181, G.182, L.183, D.203, L.204, R.208, S.223, F.246, V.247, T.252, V.269, G.270, I.271, P.293, Y.294, W.295, R.340 Chain D: F.281 Ligands: ZN.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:H.39, A:V.180, A:G.182, A:L.183, A:L.204, A:S.223, A:I.271, A:P.293, A:W.295, A:R.340 Water bridges: A:G.181, A:G.184 Salt bridges: A:H.39, A:R.340 NAD.4: 29 residues within 4Å: Chain B: C.38, H.39, S.40, D.153, T.157, I.178, G.179, V.180, G.181, G.182, L.183, D.203, L.204, R.208, S.223, F.246, V.247, T.252, V.269, G.270, I.271, P.293, Y.294, W.295, L.332, R.340 Chain C: F.281 Ligands: ZN.5, BU1.6 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.157, B:L.183 Hydrogen bonds: B:H.39, B:V.180, B:G.182, B:L.183, B:L.204, B:S.223, B:S.223, B:I.271, B:P.293, B:W.295, B:R.340 Water bridges: B:G.181 Salt bridges: B:H.39, B:R.340 NAD.8: 30 residues within 4Å: Chain B: F.281 Chain C: C.38, H.39, S.40, D.153, T.157, I.178, G.179, V.180, G.181, G.182, L.183, V.202, D.203, L.204, R.208, S.223, F.246, V.247, T.252, V.269, G.270, I.271, P.293, Y.294, W.295, L.332, R.340 Ligands: ZN.9, BU1.11 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:T.157, C:L.183 Hydrogen bonds: C:H.39, C:V.180, C:G.182, C:L.183, C:L.204, C:S.223, C:S.223, C:I.271, C:P.293, C:W.295 Water bridges: C:G.181 Salt bridges: C:H.39, C:R.340 NAD.12: 30 residues within 4Å: Chain A: F.281 Chain D: C.38, H.39, S.40, D.153, T.157, I.178, G.179, V.180, G.181, G.182, L.183, V.202, D.203, L.204, R.208, S.223, F.246, V.247, T.252, V.269, G.270, I.271, P.293, Y.294, W.295, L.332, R.340 Ligands: ZN.13, BU1.14 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:T.157, D:L.183 Hydrogen bonds: D:H.39, D:V.180, D:V.180, D:G.182, D:L.183, D:L.204, D:S.223, D:I.271, D:P.293, D:W.295 Water bridges: D:G.181, D:G.184, D:R.208 Salt bridges: D:H.39, D:R.340

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.38, S.40, H.62, D.153 Ligands: NAD.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.62, A:D.153 ZN.3: 5 residues within 4Å: Chain A: C.92, G.93, C.95, C.98, C.106 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.92, A:C.95, A:C.98, A:C.106 ZN.5: 6 residues within 4Å: Chain B: C.38, S.40, H.62, D.153 Ligands: NAD.4, BU1.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.38, B:H.62, B:D.153 ZN.7: 5 residues within 4Å: Chain B: C.92, G.93, C.95, C.98, C.106 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.92, B:C.95, B:C.98, B:C.106 ZN.9: 6 residues within 4Å: Chain C: C.38, S.40, H.62, D.153 Ligands: NAD.8, BU1.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.38, C:H.62, C:D.153 ZN.10: 5 residues within 4Å: Chain C: C.92, G.93, C.95, C.98, C.106 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.92, C:C.95, C:C.98, C:C.106 ZN.13: 6 residues within 4Å: Chain D: C.38, S.40, H.62, D.153 Ligands: NAD.12, BU1.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.38, D:H.62, D:D.153 ZN.15: 5 residues within 4Å: Chain D: C.92, G.93, C.95, C.98, C.106 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.92, D:C.95, D:C.98, D:C.106

3 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.6: 5 residues within 4Å: Chain B: S.40, I.271, Y.294 Ligands: NAD.4, ZN.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.271 Hydrogen bonds: B:S.40 BU1.11: 6 residues within 4Å: Chain C: S.40, H.62, D.153, I.271 Ligands: NAD.8, ZN.9 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.271 Hydrogen bonds: C:S.40 BU1.14: 5 residues within 4Å: Chain D: S.40, H.62, D.153 Ligands: NAD.12, ZN.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karabec, M. et al., Structural Insights Into Substrate Specificity and Solvent Tolerance in Alcohol Dehydrogenase Adh-'A' from Rhodococcus Ruber Dsm 44541. Chem.Commun.(Camb.) (2010)

Release Date

2010-08-11

Peptides

SECONDARY ALCOHOL DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

SECONDARY ALCOHOL DEHYDROGENASE

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