SMTL ID : 8gob.1

Crystal Structure of Glycerol Dehydrogenase in the presence of NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 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, TRS.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: 5 residues within 4Å: Chain B: D.121, D.171, H.254, H.271 Ligands: TRS.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.171, B:D.171, B:H.254, B:H.271 ZN.8: 6 residues within 4Å: Chain C: D.121, D.171, H.254, H.271 Ligands: NAD.9, TRS.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.171, C:D.171, C:H.254, C:H.271 ZN.12: 5 residues within 4Å: Chain D: D.121, D.171, H.254, H.271 Ligands: TRS.14 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.171, D:D.171, D:H.254, D:H.271 ZN.15: 6 residues within 4Å: Chain E: D.121, D.171, H.254, H.271 Ligands: NAD.16, TRS.17 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.171, E:D.171, E:H.254, E:H.271 ZN.19: 5 residues within 4Å: Chain F: D.121, D.171, H.254, H.271 Ligands: TRS.21 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.171, F:D.171, F:H.254, F:H.271 ZN.22: 6 residues within 4Å: Chain G: D.121, D.171, H.254, H.271 Ligands: NAD.23, TRS.24 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.171, G:D.171, G:H.254, G:H.271 ZN.26: 5 residues within 4Å: Chain H: D.121, D.171, H.254, H.271 Ligands: TRS.28 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.171, H:D.171, H:H.254, H:H.271

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

NAD.2: 27 residues within 4Å: Chain A: D.37, F.39, V.40, F.43, G.93, G.94, K.95, D.98, 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, TRS.3, TRS.4 15 PLIP interactions: 15 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:D.98, A:S.119, A:S.125, A:Y.131, A:I.156 Water bridges: A:F.39, A:T.120, A:H.271, A:H.271 NAD.6: 26 residues within 4Å: Chain B: 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: TRS.7 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.122 Hydrogen bonds: B:D.37, B:G.94, B:K.95, B:K.95, B:K.95, B:T.96, B:D.98, B:K.101, B:T.116, B:T.116, B:S.119, B:S.125, B:Y.131, B:Y.131 Water bridges: B:D.37, B:G.93, B:H.271, B:H.271 NAD.9: 27 residues within 4Å: Chain C: D.37, F.39, V.40, F.43, G.93, G.94, K.95, D.98, 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.8, TRS.10, TRS.11 15 PLIP interactions: 15 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:D.98, C:S.119, C:S.125, C:Y.131, C:I.156 Water bridges: C:F.39, C:T.120, C:H.271, C:H.271 NAD.13: 26 residues within 4Å: Chain D: 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: TRS.14 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:A.122 Hydrogen bonds: D:D.37, D:G.94, D:K.95, D:K.95, D:K.95, D:T.96, D:D.98, D:K.101, D:T.116, D:T.116, D:S.119, D:S.125, D:Y.131, D:Y.131 Water bridges: D:D.37, D:G.93, D:H.271, D:H.271 NAD.16: 27 residues within 4Å: Chain E: D.37, F.39, V.40, F.43, G.93, G.94, K.95, D.98, 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.15, TRS.17, TRS.18 15 PLIP interactions: 15 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:D.98, E:S.119, E:S.125, E:Y.131, E:I.156 Water bridges: E:F.39, E:T.120, E:H.271, E:H.271 NAD.20: 26 residues within 4Å: Chain F: 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: TRS.21 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:A.122 Hydrogen bonds: F:D.37, F:G.94, F:K.95, F:K.95, F:K.95, F:T.96, F:D.98, F:K.101, F:T.116, F:T.116, F:S.119, F:S.125, F:Y.131, F:Y.131 Water bridges: F:D.37, F:G.93, F:H.271, F:H.271 NAD.23: 27 residues within 4Å: Chain G: D.37, F.39, V.40, F.43, G.93, G.94, K.95, D.98, 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.22, TRS.24, TRS.25 15 PLIP interactions: 15 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:D.98, G:S.119, G:S.125, G:Y.131, G:I.156 Water bridges: G:F.39, G:T.120, G:H.271, G:H.271 NAD.27: 26 residues within 4Å: Chain H: 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: TRS.28 19 PLIP interactions: 19 interactions with chain H Hydrophobic interactions: H:A.122 Hydrogen bonds: H:D.37, H:G.94, H:K.95, H:K.95, H:K.95, H:T.96, H:D.98, H:K.101, H:T.116, H:T.116, H:S.119, H:S.125, H:Y.131, H:Y.131 Water bridges: H:D.37, H:G.93, H:H.271, H:H.271

12 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 8 residues within 4Å: Chain A: D.121, D.171, F.245, L.250, H.254, H.271 Ligands: ZN.1, NAD.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.121 Water bridges: A:Y.140 TRS.4: 7 residues within 4Å: Chain A: K.95, Y.131, H.257, T.261, H.271, K.274 Ligands: NAD.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.95, A:K.95, A:Y.131, A:Y.131, A:K.274 TRS.7: 9 residues within 4Å: Chain B: D.121, L.127, Y.140, F.245, L.250, H.254, H.271 Ligands: ZN.5, NAD.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.121, B:Y.140 TRS.10: 8 residues within 4Å: Chain C: D.121, D.171, F.245, L.250, H.254, H.271 Ligands: ZN.8, NAD.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.121 Water bridges: C:Y.140 TRS.11: 7 residues within 4Å: Chain C: K.95, Y.131, H.257, T.261, H.271, K.274 Ligands: NAD.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.95, C:K.95, C:Y.131, C:Y.131, C:K.274 TRS.14: 9 residues within 4Å: Chain D: D.121, L.127, Y.140, F.245, L.250, H.254, H.271 Ligands: ZN.12, NAD.13 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.121, D:Y.140 TRS.17: 8 residues within 4Å: Chain E: D.121, D.171, F.245, L.250, H.254, H.271 Ligands: ZN.15, NAD.16 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.121, E:H.271 Water bridges: E:Y.140 TRS.18: 7 residues within 4Å: Chain E: K.95, Y.131, H.257, T.261, H.271, K.274 Ligands: NAD.16 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:K.95, E:K.95, E:Y.131, E:Y.131, E:K.274 TRS.21: 9 residues within 4Å: Chain F: D.121, L.127, Y.140, F.245, L.250, H.254, H.271 Ligands: ZN.19, NAD.20 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.121, F:Y.140 TRS.24: 8 residues within 4Å: Chain G: D.121, D.171, F.245, L.250, H.254, H.271 Ligands: ZN.22, NAD.23 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.121 Water bridges: G:Y.140 TRS.25: 7 residues within 4Å: Chain G: K.95, Y.131, H.257, T.261, H.271, K.274 Ligands: NAD.23 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:K.95, G:K.95, G:Y.131, G:Y.131, G:K.274 TRS.28: 9 residues within 4Å: Chain H: D.121, L.127, Y.140, F.245, L.250, H.254, H.271 Ligands: ZN.26, NAD.27 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:D.121, H:Y.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, T. et al., Structural and functional insights into the flexible beta-hairpin of glycerol dehydrogenase. Febs J. (2023)

Release Date

2023-06-14

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

Related Entries With Identical Sequence