SMTL ID : 1y9a.1

Alcohol Dehydrogenase from Entamoeba histolotica in complex with cacodylate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.37, S.39, H.59, D.150 Ligands: CAC.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.37, A:H.59, A:D.150 ZN.3: 2 residues within 4Å: Chain A: D.51, H.53 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.51, A:D.51, A:H.53, H2O.13 ZN.7: 5 residues within 4Å: Chain B: C.37, S.39, H.59, D.150 Ligands: CAC.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.37, B:H.59, B:D.150 ZN.9: 2 residues within 4Å: Chain B: D.51, H.53 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.51, B:D.51, B:H.53 ZN.16: 5 residues within 4Å: Chain C: C.37, S.39, H.59, D.150 Ligands: CAC.17 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.37, C:H.59, C:D.150 ZN.18: 2 residues within 4Å: Chain C: D.51, H.53 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.51, C:D.51, C:H.53, H2O.42 ZN.22: 5 residues within 4Å: Chain D: C.37, S.39, H.59, D.150 Ligands: CAC.23 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.37, D:H.59, D:D.150 ZN.24: 2 residues within 4Å: Chain D: D.51, H.53 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.51, D:D.51, D:H.53

4 x CAC: CACODYLATE ION(Non-covalent)

CAC.2: 9 residues within 4Å: Chain A: C.37, S.39, H.59, I.86, W.110, D.150, T.154 Chain C: M.285 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.39, A:T.154 CAC.8: 11 residues within 4Å: Chain B: C.37, S.39, H.59, A.85, I.86, W.110, D.150, T.154, L.294 Chain D: M.285 Ligands: ZN.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.39 CAC.17: 9 residues within 4Å: Chain A: M.285 Chain C: C.37, S.39, H.59, I.86, W.110, D.150, T.154 Ligands: ZN.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.39 CAC.23: 11 residues within 4Å: Chain B: M.285 Chain D: C.37, S.39, H.59, A.85, I.86, W.110, D.150, T.154, L.294 Ligands: ZN.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.39, D:T.154

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: C.22, G.23, P.24, G.69, S.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.23, A:S.70 ACT.10: 4 residues within 4Å: Chain B: C.22, P.24, G.69, S.70 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.70 Water bridges: B:C.22, B:V.68 ACT.19: 5 residues within 4Å: Chain C: C.22, G.23, P.24, G.69, S.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.23, C:S.70 ACT.25: 4 residues within 4Å: Chain D: C.22, P.24, G.69, S.70 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.70 Water bridges: D:C.22, D:V.68

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain A: H.360 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.360, H2O.1, H2O.1 MG.11: 4 residues within 4Å: Chain B: G.167, T.169, D.237 Chain C: K.304 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.167, H2O.14, H2O.15 MG.20: 1 residues within 4Å: Chain C: H.360 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.360, H2O.30, H2O.30 MG.26: 4 residues within 4Å: Chain A: K.304 Chain D: G.167, T.169, D.237 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:G.167, H2O.43, H2O.44

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: G.98, Y.99, M.101, H.157 Chain C: H.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.98, A:H.157 EDO.12: 6 residues within 4Å: Chain B: G.98, Y.99, P.100, M.101, H.157 Chain D: H.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.98, B:H.157 EDO.13: 2 residues within 4Å: Chain B: I.206, K.318 No protein-ligand interaction detected (PLIP) EDO.14: 7 residues within 4Å: Chain B: D.261, H.289, H.291 Chain D: D.261, H.289, H.291 Ligands: EDO.29 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:D.261, B:H.291, D:H.289 EDO.15: 4 residues within 4Å: Chain B: N.187, H.188 Chain C: N.187, H.188 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:H.188, B:H.188 Water bridges: C:N.187, B:N.187 EDO.21: 5 residues within 4Å: Chain A: H.287 Chain C: G.98, Y.99, M.101, H.157 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.98, C:H.157 EDO.27: 6 residues within 4Å: Chain B: H.287 Chain D: G.98, Y.99, P.100, M.101, H.157 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.98, D:H.157 Water bridges: B:H.287 EDO.28: 2 residues within 4Å: Chain D: I.206, K.318 No protein-ligand interaction detected (PLIP) EDO.29: 7 residues within 4Å: Chain B: D.261, H.289, H.291 Chain D: D.261, H.289, H.291 Ligands: EDO.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:H.289, D:D.261 EDO.30: 4 residues within 4Å: Chain A: N.187, H.188 Chain D: N.187, H.188 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:H.188, A:H.188 Water bridges: D:N.187, A:N.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimon, L.J. et al., Structure of alcohol dehydrogenase from Entamoeba histolytica. Acta Crystallogr.,Sect.D (2006)

Release Date

2006-01-17

Peptides

NADP-dependent alcohol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

NADP-dependent alcohol dehydrogenase