SMTL ID : 7kc2.1

Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NADH

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.2: 5 residues within 4Å: Chain A: C.43, T.45, H.66, C.153 Ligands: NAD.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.43, A:H.66, A:C.153 ZN.4: 4 residues within 4Å: Chain B: C.97, 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.5: 5 residues within 4Å: Chain B: C.43, T.45, H.66, C.153 Ligands: NAD.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.43, B:H.66, B:C.153 ZN.7: 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.8: 5 residues within 4Å: Chain C: C.43, T.45, H.66, C.153 Ligands: NAD.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.43, C:H.66, C:C.153 ZN.10: 4 residues within 4Å: Chain D: C.97, 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 ZN.11: 5 residues within 4Å: Chain D: C.43, T.45, H.66, C.153 Ligands: NAD.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.43, D:H.66, D:C.153

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

NAD.3: 33 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, G.202, 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, I.337, R.340 Chain D: V.284 Ligands: ZN.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.157 Hydrogen bonds: A:H.44, A:H.48, A:A.179, A:G.181, A:L.182, A:K.206, A:K.206, A:S.248, A:S.248, A:V.268, A:M.270 Salt bridges: A:H.44, A:H.44, A:R.340 pi-Stacking: A:F.221, A:F.221 NAD.6: 33 residues within 4Å: Chain B: 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, G.202, 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, I.337, R.340 Chain C: V.284 Ligands: ZN.5 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.157 Hydrogen bonds: B:H.44, B:H.48, B:A.179, B:G.181, B:L.182, B:K.206, B:K.206, B:S.248, B:S.248, B:V.268, B:M.270 Salt bridges: B:H.44, B:H.44, B:R.340 pi-Stacking: B:F.221, B:F.221 NAD.9: 33 residues within 4Å: Chain B: V.284 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, G.202, 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, I.337, R.340 Ligands: ZN.8 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:T.157 Hydrogen bonds: C:H.44, C:T.45, C:H.48, C:A.179, C:G.181, C:L.182, C:K.206, C:K.206, C:S.248, C:S.248, C:V.268, C:M.270 Salt bridges: C:H.44, C:H.44, C:R.340 pi-Stacking: C:F.221, C:F.221 NAD.12: 33 residues within 4Å: Chain A: V.284 Chain D: 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, G.202, 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, I.337, R.340 Ligands: ZN.11 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:T.157 Hydrogen bonds: D:H.44, D:T.45, D:H.48, D:A.179, D:G.181, D:L.182, D:K.206, D:K.206, D:S.248, D:S.248, D:V.268, D:M.270 Salt bridges: D:H.44, D:H.44, D:R.340 pi-Stacking: D:F.221, D:F.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guntupalli, S.R. et al., Cryo-Electron Microscopy Structures of Yeast Alcohol Dehydrogenase. Biochemistry (2021)

Release Date

2021-03-31

Peptides

Alcohol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Alcohol dehydrogenase