SMTL ID : 8x6m.1

Crystal Structure of Glycerol Dehydrogenase in the Presence of NAD+ and Glycerol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.121, D.171, H.254, H.271 Ligands: NAD.2, GOL.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.171, A:D.171, A:H.254, A:H.271 ZN.5: 4 residues within 4Å: Chain B: D.121, D.171, H.254, H.271 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.171, B:D.171, B:H.254, B:H.271, H2O.11 ZN.7: 6 residues within 4Å: Chain C: D.121, D.171, H.254, H.271 Ligands: NAD.8, GOL.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.171, C:D.171, C:H.254, C:H.271 ZN.11: 4 residues within 4Å: Chain D: D.121, D.171, H.254, H.271 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.171, D:D.171, D:H.254, D:H.271, H2O.27 ZN.13: 6 residues within 4Å: Chain E: D.121, D.171, H.254, H.271 Ligands: NAD.14, GOL.15 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.171, E:D.171, E:H.254, E:H.271 ZN.17: 4 residues within 4Å: Chain F: D.121, D.171, H.254, H.271 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.171, F:D.171, F:H.254, F:H.271, H2O.44 ZN.19: 6 residues within 4Å: Chain G: D.121, D.171, H.254, H.271 Ligands: NAD.20, GOL.21 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.171, G:D.171, G:H.254, G:H.271 ZN.23: 4 residues within 4Å: Chain H: D.121, D.171, H.254, H.271 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.171, H:D.171, H:H.254, H:H.271, H2O.60

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

NAD.2: 28 residues within 4Å: Chain A: D.37, F.39, V.40, F.43, G.93, G.94, K.95, D.98, K.101, T.116, I.117, S.119, T.120, D.121, A.122, S.125, L.127, V.129, Y.131, I.156, A.160, P.161, L.164, F.245, H.271 Ligands: ZN.1, GOL.3, GOL.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.122 Hydrogen bonds: A:D.37, A:G.94, A:K.95, A:K.95, A:K.95, A:T.96, A:D.98, A:T.116, A:S.119, A:S.125, A:Y.131 Water bridges: A:D.37, A:G.93, A:S.119, A:V.129 NAD.6: 17 residues within 4Å: Chain B: F.39, V.40, F.43, G.93, G.94, K.95, T.116, I.117, S.119, T.120, I.156, G.159, A.160, P.161, L.164, Y.270, H.271 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.270, B:Y.270, B:H.271 Hydrogen bonds: B:G.94, B:K.95, B:T.116, B:T.116, B:S.119 Water bridges: B:G.93, B:G.93, B:G.93, B:T.96, B:H.271, B:K.274 NAD.8: 28 residues within 4Å: Chain C: D.37, F.39, V.40, F.43, G.93, G.94, K.95, D.98, K.101, T.116, I.117, S.119, T.120, D.121, A.122, S.125, L.127, V.129, Y.131, I.156, A.160, P.161, L.164, F.245, H.271 Ligands: ZN.7, GOL.9, GOL.10 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:A.122 Hydrogen bonds: C:D.37, C:G.94, C:K.95, C:K.95, C:K.95, C:T.96, C:D.98, C:T.116, C:S.119, C:S.125, C:Y.131 Water bridges: C:D.37, C:G.93, C:S.119, C:V.129 NAD.12: 17 residues within 4Å: Chain D: F.39, V.40, F.43, G.93, G.94, K.95, T.116, I.117, S.119, T.120, I.156, G.159, A.160, P.161, L.164, Y.270, H.271 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:Y.270, D:Y.270, D:H.271 Hydrogen bonds: D:G.94, D:K.95, D:T.116, D:T.116, D:S.119 Water bridges: D:G.93, D:G.93, D:G.93, D:T.96, D:H.271, D:K.274 NAD.14: 28 residues within 4Å: Chain E: D.37, F.39, V.40, F.43, G.93, G.94, K.95, D.98, K.101, T.116, I.117, S.119, T.120, D.121, A.122, S.125, L.127, V.129, Y.131, I.156, A.160, P.161, L.164, F.245, H.271 Ligands: ZN.13, GOL.15, GOL.16 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:A.122 Hydrogen bonds: E:D.37, E:G.94, E:K.95, E:K.95, E:K.95, E:T.96, E:D.98, E:T.116, E:S.119, E:S.125, E:Y.131 Water bridges: E:D.37, E:G.93, E:S.119, E:V.129 NAD.18: 17 residues within 4Å: Chain F: F.39, V.40, F.43, G.93, G.94, K.95, T.116, I.117, S.119, T.120, I.156, G.159, A.160, P.161, L.164, Y.270, H.271 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:Y.270, F:Y.270, F:H.271 Hydrogen bonds: F:G.94, F:K.95, F:T.116, F:T.116, F:S.119 Water bridges: F:G.93, F:G.93, F:G.93, F:T.96, F:H.271, F:K.274 NAD.20: 28 residues within 4Å: Chain G: D.37, F.39, V.40, F.43, G.93, G.94, K.95, D.98, K.101, T.116, I.117, S.119, T.120, D.121, A.122, S.125, L.127, V.129, Y.131, I.156, A.160, P.161, L.164, F.245, H.271 Ligands: ZN.19, GOL.21, GOL.22 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:A.122 Hydrogen bonds: G:D.37, G:G.94, G:K.95, G:K.95, G:K.95, G:T.96, G:D.98, G:T.116, G:S.119, G:S.125, G:Y.131 Water bridges: G:D.37, G:G.93, G:S.119, G:V.129 NAD.24: 17 residues within 4Å: Chain H: F.39, V.40, F.43, G.93, G.94, K.95, T.116, I.117, S.119, T.120, I.156, G.159, A.160, P.161, L.164, Y.270, H.271 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:Y.270, H:Y.270, H:H.271 Hydrogen bonds: H:G.94, H:K.95, H:T.116, H:T.116, H:S.119 Water bridges: H:G.93, H:G.93, H:G.93, H:T.96, H:H.271, H:K.274

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: D.121, Y.140, F.245, H.254, H.271 Ligands: ZN.1, NAD.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.140, A:Y.140, A:H.271 GOL.4: 7 residues within 4Å: Chain A: Y.131, H.257, T.261, H.267, H.271, K.274 Ligands: NAD.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.131, A:Y.131, A:H.257, A:K.274 GOL.9: 7 residues within 4Å: Chain C: D.121, Y.140, F.245, H.254, H.271 Ligands: ZN.7, NAD.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.140, C:Y.140, C:H.271 GOL.10: 7 residues within 4Å: Chain C: Y.131, H.257, T.261, H.267, H.271, K.274 Ligands: NAD.8 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.131, C:Y.131, C:H.257, C:K.274 GOL.15: 7 residues within 4Å: Chain E: D.121, Y.140, F.245, H.254, H.271 Ligands: ZN.13, NAD.14 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.140, E:Y.140, E:H.271 GOL.16: 7 residues within 4Å: Chain E: Y.131, H.257, T.261, H.267, H.271, K.274 Ligands: NAD.14 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Y.131, E:Y.131, E:H.257, E:K.274 GOL.21: 7 residues within 4Å: Chain G: D.121, Y.140, F.245, H.254, H.271 Ligands: ZN.19, NAD.20 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Y.140, G:Y.140, G:H.271 GOL.22: 7 residues within 4Å: Chain G: Y.131, H.257, T.261, H.267, H.271, K.274 Ligands: NAD.20 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Y.131, G:Y.131, G:H.257, G:K.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, T. et al., Structural insights into the octamerization of glycerol dehydrogenase. Plos One (2024)

Release Date

2024-03-27

Peptides

Glycerol dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Glycerol dehydrogenase

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