SMTL ID : 3ce9.1

Crystal structure of glycerol dehydrogenase (NP_348253.1) from Clostridium acetobutylicum at 2.37 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.125, D.172, H.251, H.267 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.172, A:H.251, A:H.267, H2O.2, H2O.3 ZN.6: 4 residues within 4Å: Chain B: D.125, D.172, H.251, H.267 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.172, B:H.251, B:H.267, H2O.4, H2O.4 ZN.8: 4 residues within 4Å: Chain C: D.125, D.172, H.251, H.267 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.172, C:H.251, C:H.267, H2O.5, H2O.6 ZN.15: 4 residues within 4Å: Chain D: D.125, D.172, H.251, H.267 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.172, D:D.172, D:H.251, D:H.267, H2O.7

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

EDO.2: 6 residues within 4Å: Chain A: G.97, T.120, S.121, S.161, P.162, F.165 No protein-ligand interaction detected (PLIP) EDO.3: 4 residues within 4Å: Chain A: E.43, G.44, I.45, L.48 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: F.41, Y.46, V.67, E.68, T.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.68, A:T.69 EDO.7: 4 residues within 4Å: Chain B: G.97, T.120, S.121, F.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.120 EDO.9: 3 residues within 4Å: Chain C: Y.181, F.185, E.188 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain C: E.43, G.44, I.45, L.48 No protein-ligand interaction detected (PLIP) EDO.11: 1 residues within 4Å: Chain C: F.49 No protein-ligand interaction detected (PLIP) EDO.12: 6 residues within 4Å: Chain C: W.183, E.186, S.192, N.242, S.244, R.326 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.183, C:S.192, C:S.244, C:R.326 EDO.13: 7 residues within 4Å: Chain B: K.112 Chain C: P.130, V.131, P.144, M.237, N.242, S.243 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.243 EDO.14: 3 residues within 4Å: Chain C: F.185, Y.329, N.335 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.329, C:Y.329, C:N.335 EDO.16: 3 residues within 4Å: Chain D: S.310, D.311, R.314 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.310, D:R.314 EDO.17: 5 residues within 4Å: Chain D: G.97, G.98, K.99, A.100, F.165 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.97, D:G.98, D:K.99, D:A.100 EDO.18: 5 residues within 4Å: Chain D: F.41, Y.46, V.67, E.68, T.69 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain D: Y.181, K.184, F.185, E.188 No protein-ligand interaction detected (PLIP) EDO.20: 3 residues within 4Å: Chain D: N.189, K.191, Y.327 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.189

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: Y.40, E.68, T.69, V.70, N.81, M.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.81 PEG.21: 6 residues within 4Å: Chain D: K.283, H.284, R.285, E.286, E.287, R.288 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.283, D:R.285, D:E.286, D:E.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of glycerol dehydrogenase (NP_348253.1) from Clostridium acetobutylicum at 2.37 A resolution. To be published

Release Date

2008-03-11

Peptides

Glycerol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glycerol dehydrogenase