SMTL ID : 5env.1

YEAST ALCOHOL DEHYDROGENASE WITH BOUND COENZYME

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.43, T.45, H.66, C.153 Ligands: NAD.3, ETF.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.43, A:H.66, A:C.153, ETF.4 ZN.2: 4 residues within 4Å: Chain A: C.97, C.100, C.103, C.111 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.97, A:C.100, A:C.103, A:C.111 ZN.5: 5 residues within 4Å: Chain B: C.43, H.66, E.67, C.153 Ligands: ETF.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.43, B:H.66, B:E.67, B:C.153 ZN.6: 5 residues within 4Å: Chain B: C.97, M.98, C.100, C.103, C.111 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.97, B:C.100, B:C.103, B:C.111 ZN.9: 6 residues within 4Å: Chain C: C.43, T.45, H.66, C.153 Ligands: NAD.11, ETF.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:C.43, C:H.66, C:C.153, ETF.12 ZN.10: 4 residues within 4Å: Chain C: C.97, C.100, C.103, C.111 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.97, C:C.100, C:C.103, C:C.111 ZN.13: 5 residues within 4Å: Chain D: C.43, H.66, E.67, C.153 Ligands: ETF.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.43, D:H.66, D:E.67, D:C.153 ZN.14: 5 residues within 4Å: Chain D: C.97, M.98, C.100, C.103, C.111 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.97, D:C.100, D:C.103, D:C.111

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

NAD.3: 31 residues within 4Å: Chain A: C.43, H.44, T.45, H.48, W.54, C.153, T.157, S.176, G.177, A.179, G.180, G.181, L.182, I.200, D.201, K.206, F.221, V.245, S.246, S.248, A.251, V.268, G.269, M.270, S.293, Y.294, V.295, R.340 Chain B: V.284 Ligands: ZN.1, ETF.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.157, A:L.182, A:V.268 Hydrogen bonds: A:H.44, A:T.45, A:H.48, A:A.179, A:G.181, A:L.182, A:K.206, A:S.248, A:V.268, A:M.270, A:V.295 Water bridges: A:G.180, A:G.183 Salt bridges: A:H.44, A:R.340 pi-Stacking: A:F.221 NAD.7: 26 residues within 4Å: Chain A: V.284 Chain B: H.44, T.157, S.176, G.177, A.179, G.180, G.181, L.182, I.200, D.201, K.206, F.221, V.245, S.246, V.247, S.248, A.251, V.268, G.269, M.270, S.293, Y.294, V.295, R.340 Ligands: ETF.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.181, B:L.182, B:K.206, B:K.206, B:S.248, B:S.248, B:M.270, B:S.293, B:R.340 Salt bridges: B:H.44 NAD.11: 31 residues within 4Å: Chain C: C.43, H.44, T.45, H.48, W.54, C.153, T.157, S.176, G.177, A.179, G.180, G.181, L.182, I.200, D.201, K.206, F.221, V.245, S.246, S.248, A.251, V.268, G.269, M.270, S.293, Y.294, V.295, R.340 Chain D: V.284 Ligands: ZN.9, ETF.12 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:T.157, C:L.182, C:V.268 Hydrogen bonds: C:H.44, C:H.48, C:A.179, C:G.181, C:L.182, C:K.206, C:S.248, C:V.268, C:M.270, C:V.295 Water bridges: C:G.180, C:G.183 Salt bridges: C:H.44, C:R.340 pi-Stacking: C:F.221 NAD.15: 26 residues within 4Å: Chain C: V.284 Chain D: H.44, T.157, S.176, G.177, A.179, G.180, G.181, L.182, I.200, D.201, K.206, F.221, V.245, S.246, V.247, S.248, A.251, V.268, G.269, M.270, S.293, Y.294, V.295, R.340 Ligands: ETF.16 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.181, D:L.182, D:K.206, D:K.206, D:S.248, D:S.248, D:M.270, D:S.293, D:R.340 Salt bridges: D:H.44

4 x ETF: TRIFLUOROETHANOL(Non-covalent)

ETF.4: 11 residues within 4Å: Chain A: C.43, T.45, W.54, H.66, W.92, C.153, M.270, Y.294, V.295 Ligands: ZN.1, NAD.3 No protein-ligand interaction detected (PLIP) ETF.8: 8 residues within 4Å: Chain B: T.45, H.66, W.92, C.153, Y.294, V.295 Ligands: ZN.5, NAD.7 No protein-ligand interaction detected (PLIP) ETF.12: 11 residues within 4Å: Chain C: C.43, T.45, W.54, H.66, W.92, C.153, M.270, Y.294, V.295 Ligands: ZN.9, NAD.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.45 ETF.16: 8 residues within 4Å: Chain D: T.45, H.66, W.92, C.153, Y.294, V.295 Ligands: ZN.13, NAD.15 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.45, D:H.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plapp, B.V. et al., Mechanistic implications from structures of yeast alcohol dehydrogenase complexed with coenzyme and an alcohol. Arch.Biochem.Biophys. (2015)

Release Date

2015-11-25

Peptides

Alcohol dehydrogenase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Alcohol dehydrogenase 1

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