SMTL ID : 1jq5.1

Bacillus Stearothermophilus Glycerol dehydrogenase complex with NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-octamer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.123, D.173, H.256, H.274 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.173, A:D.173, A:H.256, A:H.274, H2O.1 ZN.2: 2 residues within 4Å: Chain A: E.268, H.271 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.268, A:H.271 ZN.4: 4 residues within 4Å: Chain B: D.123, D.173, H.256, H.274 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.173, B:D.173, B:H.256, B:H.274, H2O.11 ZN.5: 2 residues within 4Å: Chain B: E.268, H.271 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.268, B:H.271 ZN.7: 4 residues within 4Å: Chain C: D.123, D.173, H.256, H.274 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.173, C:D.173, C:H.256, C:H.274, H2O.21 ZN.8: 2 residues within 4Å: Chain C: E.268, H.271 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.268, C:H.271 ZN.10: 4 residues within 4Å: Chain D: D.123, D.173, H.256, H.274 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.173, D:D.173, D:H.256, D:H.274, H2O.32 ZN.11: 2 residues within 4Å: Chain D: E.268, H.271 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.268, D:H.271 ZN.13: 4 residues within 4Å: Chain E: D.123, D.173, H.256, H.274 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.173, E:D.173, E:H.256, E:H.274, H2O.42 ZN.14: 2 residues within 4Å: Chain E: E.268, H.271 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.268, E:H.271 ZN.16: 4 residues within 4Å: Chain F: D.123, D.173, H.256, H.274 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.173, F:D.173, F:H.256, F:H.274, H2O.53 ZN.17: 2 residues within 4Å: Chain F: E.268, H.271 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.268, F:H.271 ZN.19: 4 residues within 4Å: Chain G: D.123, D.173, H.256, H.274 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.173, G:D.173, G:H.256, G:H.274, H2O.63 ZN.20: 2 residues within 4Å: Chain G: E.268, H.271 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.268, G:H.271 ZN.22: 4 residues within 4Å: Chain H: D.123, D.173, H.256, H.274 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.173, H:D.173, H:H.256, H:H.274, H2O.73 ZN.23: 2 residues within 4Å: Chain H: E.268, H.271 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.268, H:H.271

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

NAD.3: 25 residues within 4Å: Chain A: D.39, I.41, V.42, I.45, G.95, G.96, K.97, D.100, K.103, T.118, S.121, T.122, D.123, A.124, S.127, L.129, S.130, V.131, Y.133, A.162, P.163, L.166, D.173, F.247, H.274 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:A.124 Hydrogen bonds: A:D.39, A:G.96, A:K.97, A:K.97, A:K.97, A:D.100, A:T.118, A:T.118, A:S.121, A:S.121, A:S.127, A:Y.133, A:Y.133 Water bridges: A:G.95, A:G.95, A:T.122, A:V.131, A:H.274, A:H.274 pi-Stacking: A:H.274 NAD.6: 25 residues within 4Å: Chain B: D.39, I.41, V.42, I.45, G.95, G.96, K.97, D.100, K.103, T.118, S.121, T.122, D.123, A.124, S.127, L.129, S.130, V.131, Y.133, A.162, P.163, L.166, D.173, F.247, H.274 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:A.124 Hydrogen bonds: B:D.39, B:G.96, B:K.97, B:K.97, B:K.97, B:D.100, B:T.118, B:T.118, B:S.121, B:S.121, B:S.127, B:Y.133, B:Y.133 Water bridges: B:G.95, B:G.95, B:T.122, B:V.131, B:H.274, B:H.274 pi-Stacking: B:H.274 NAD.9: 25 residues within 4Å: Chain C: D.39, I.41, V.42, I.45, G.95, G.96, K.97, D.100, K.103, T.118, S.121, T.122, D.123, A.124, S.127, L.129, S.130, V.131, Y.133, A.162, P.163, L.166, D.173, F.247, H.274 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:A.124 Hydrogen bonds: C:D.39, C:G.96, C:K.97, C:K.97, C:K.97, C:D.100, C:T.118, C:T.118, C:S.121, C:S.121, C:S.127, C:Y.133, C:Y.133 Water bridges: C:G.95, C:G.95, C:T.122, C:V.131, C:H.274, C:H.274 pi-Stacking: C:H.274 NAD.12: 25 residues within 4Å: Chain D: D.39, I.41, V.42, I.45, G.95, G.96, K.97, D.100, K.103, T.118, S.121, T.122, D.123, A.124, S.127, L.129, S.130, V.131, Y.133, A.162, P.163, L.166, D.173, F.247, H.274 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:A.124 Hydrogen bonds: D:D.39, D:G.96, D:K.97, D:K.97, D:K.97, D:D.100, D:T.118, D:T.118, D:S.121, D:S.121, D:S.127, D:Y.133, D:Y.133 Water bridges: D:G.95, D:G.95, D:T.122, D:V.131, D:H.274, D:H.274 pi-Stacking: D:H.274 NAD.15: 25 residues within 4Å: Chain E: D.39, I.41, V.42, I.45, G.95, G.96, K.97, D.100, K.103, T.118, S.121, T.122, D.123, A.124, S.127, L.129, S.130, V.131, Y.133, A.162, P.163, L.166, D.173, F.247, H.274 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:A.124 Hydrogen bonds: E:D.39, E:G.96, E:K.97, E:K.97, E:K.97, E:D.100, E:T.118, E:S.121, E:S.121, E:S.127, E:Y.133 Water bridges: E:G.95, E:G.95, E:T.122, E:V.131, E:H.274, E:H.274 pi-Stacking: E:H.274 NAD.18: 25 residues within 4Å: Chain F: D.39, I.41, V.42, I.45, G.95, G.96, K.97, D.100, K.103, T.118, S.121, T.122, D.123, A.124, S.127, L.129, S.130, V.131, Y.133, A.162, P.163, L.166, D.173, F.247, H.274 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:A.124 Hydrogen bonds: F:D.39, F:G.96, F:K.97, F:K.97, F:K.97, F:D.100, F:T.118, F:S.121, F:S.121, F:S.127, F:Y.133 Water bridges: F:G.95, F:G.95, F:T.122, F:V.131, F:H.274, F:H.274 pi-Stacking: F:H.274 NAD.21: 25 residues within 4Å: Chain G: D.39, I.41, V.42, I.45, G.95, G.96, K.97, D.100, K.103, T.118, S.121, T.122, D.123, A.124, S.127, L.129, S.130, V.131, Y.133, A.162, P.163, L.166, D.173, F.247, H.274 19 PLIP interactions: 19 interactions with chain G Hydrophobic interactions: G:A.124 Hydrogen bonds: G:D.39, G:G.96, G:K.97, G:K.97, G:K.97, G:D.100, G:T.118, G:S.121, G:S.121, G:S.127, G:Y.133 Water bridges: G:G.95, G:G.95, G:T.122, G:V.131, G:H.274, G:H.274 pi-Stacking: G:H.274 NAD.24: 25 residues within 4Å: Chain H: D.39, I.41, V.42, I.45, G.95, G.96, K.97, D.100, K.103, T.118, S.121, T.122, D.123, A.124, S.127, L.129, S.130, V.131, Y.133, A.162, P.163, L.166, D.173, F.247, H.274 19 PLIP interactions: 19 interactions with chain H Hydrophobic interactions: H:A.124 Hydrogen bonds: H:D.39, H:G.96, H:K.97, H:K.97, H:K.97, H:D.100, H:T.118, H:S.121, H:S.121, H:S.127, H:Y.133 Water bridges: H:G.95, H:G.95, H:T.122, H:V.131, H:H.274, H:H.274 pi-Stacking: H:H.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruzheinikov, S.N. et al., Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase. Structure (2001)

Release Date

2001-10-01

Peptides

Glycerol dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Glycerol dehydrogenase

Related Entries With Identical Sequence