SMTL ID : 2oui.1

D275P mutant of alcohol dehydrogenase from protozoa Entamoeba histolytica

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.37, S.39, H.59, D.150 Ligands: CAC.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.37, A:H.59, A:D.150 ZN.10: 5 residues within 4Å: Chain B: C.37, S.39, H.59, D.150 Ligands: CAC.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.37, B:H.59, B:D.150 ZN.18: 5 residues within 4Å: Chain C: C.37, S.39, H.59, D.150 Ligands: CAC.19 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.37, C:H.59, C:D.150 ZN.23: 5 residues within 4Å: Chain D: C.37, S.39, H.59, D.150 Ligands: CAC.25 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.37, D:H.59, D:D.150

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 4 residues within 4Å: Chain A: T.38, G.176, P.177, V.178 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.38, A:T.38, A:V.178 Water bridges: A:T.38, A:G.179 NO3.3: 4 residues within 4Å: Chain A: K.201, C.204, D.205, N.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.217 NO3.11: 4 residues within 4Å: Chain B: C.22, P.24, G.69, S.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.70, B:S.70 NO3.24: 2 residues within 4Å: Chain D: D.139, S.310 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.139

4 x CAC: CACODYLATE ION(Non-covalent)

CAC.4: 11 residues within 4Å: Chain A: C.37, S.39, H.59, A.85, I.86, W.110, D.150, T.154 Chain B: M.285 Ligands: ZN.1, EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.39, A:T.154 CAC.12: 9 residues within 4Å: Chain A: M.285 Chain B: C.37, S.39, H.59, I.86, W.110, D.150, T.154 Ligands: ZN.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.39 Water bridges: B:V.265 CAC.19: 10 residues within 4Å: Chain C: C.37, S.39, H.59, I.86, W.110, D.150, T.154, L.294 Chain D: M.285 Ligands: ZN.18 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.39, C:S.39 CAC.25: 9 residues within 4Å: Chain C: M.285 Chain D: C.37, S.39, H.59, I.86, W.110, D.150, T.154 Ligands: ZN.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.39, D:D.150, D:T.154

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

EDO.5: 8 residues within 4Å: Chain A: C.37, T.38, S.39, V.178, V.265, N.266, Y.267 Ligands: CAC.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.265, A:Y.267 EDO.6: 7 residues within 4Å: Chain A: G.174, I.175, G.176, G.198, S.199, R.200, C.203 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.175, A:S.199, A:S.199, A:R.200 Water bridges: A:G.176 EDO.7: 5 residues within 4Å: Chain A: E.160, L.189 Chain D: K.165, L.166 Ligands: EDO.8 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:L.166, A:E.160 Water bridges: D:L.166 EDO.8: 5 residues within 4Å: Chain A: E.160, N.163, I.164, K.165 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.160, A:K.165, A:K.165 EDO.13: 5 residues within 4Å: Chain B: D.89, W.90, G.91, E.92, E.128 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.91, B:E.92, B:E.128 EDO.14: 6 residues within 4Å: Chain B: S.95, Q.96, G.98 Chain D: G.98, P.100 Ligands: EDO.27 No protein-ligand interaction detected (PLIP) EDO.15: 5 residues within 4Å: Chain B: E.160, N.163, I.164, K.165, L.189 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.164, B:K.165 EDO.20: 4 residues within 4Å: Chain C: E.160, N.163, I.164, L.189 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.164, C:K.165 EDO.27: 4 residues within 4Å: Chain D: R.97, G.98, Y.99 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.97

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 3 residues within 4Å: Chain A: K.2, W.14, E.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.2 PGE.16: 5 residues within 4Å: Chain B: K.2, W.14, E.122, L.327, E.328 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.122 PGE.17: 4 residues within 4Å: Chain B: H.157, E.160, L.161, H.291 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.291 PGE.22: 8 residues within 4Å: Chain A: S.95, Q.96, G.98 Chain C: S.95, Q.96, R.97, G.98, P.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.98

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.21: 5 residues within 4Å: Chain C: K.2, W.14, E.16, E.122, E.328 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.2, C:E.122

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.26: 6 residues within 4Å: Chain D: H.59, E.60, A.61, V.83, P.84, V.119 Ligand excluded by PLIP

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.28: 4 residues within 4Å: Chain D: K.2, W.14, L.327, E.328 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goihberg, E. et al., Thermal stabilization of the protozoan Entamoeba histolytica alcohol dehydrogenase by a single proline substitution. Proteins (2008)

Release Date

2008-02-12

Peptides

NADP-dependent alcohol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NADP-dependent alcohol dehydrogenase