SMTL ID : 8goa.1

Crystal Structure of Glycerol Dehydrogenase in the absence of NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-octamer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.121, D.171, H.254, H.271 Ligands: TRS.2 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.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.171, B:D.171, B:H.254, B:H.271 ZN.9: 5 residues within 4Å: Chain C: D.121, D.171, H.254, H.271 Ligands: 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.13: 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.17: 5 residues within 4Å: Chain E: D.121, D.171, H.254, H.271 Ligands: TRS.18 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.171, E:D.171, E:H.254, E:H.271 ZN.21: 5 residues within 4Å: Chain F: D.121, D.171, H.254, H.271 Ligands: TRS.22 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.171, F:D.171, F:H.254, F:H.271 ZN.25: 5 residues within 4Å: Chain G: D.121, D.171, H.254, H.271 Ligands: TRS.26 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.171, G:D.171, G:H.254, G:H.271 ZN.29: 5 residues within 4Å: Chain H: D.121, D.171, H.254, H.271 Ligands: TRS.30 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.171, H:D.171, H:H.254, H:H.271

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

TRS.2: 9 residues within 4Å: Chain A: T.120, D.121, V.129, Y.140, D.171, F.245, H.254, H.271 Ligands: ZN.1 Ligand excluded by PLIP TRS.3: 6 residues within 4Å: Chain A: Y.131, H.257, T.261, H.271, K.274 Ligands: TRS.4 Ligand excluded by PLIP TRS.4: 4 residues within 4Å: Chain A: S.119, Y.270, H.271 Ligands: TRS.3 Ligand excluded by PLIP TRS.6: 9 residues within 4Å: Chain B: D.121, L.127, V.129, Y.140, D.171, F.245, H.254, H.271 Ligands: ZN.5 Ligand excluded by PLIP TRS.7: 9 residues within 4Å: Chain B: Y.131, G.135, H.257, T.261, Y.269, Y.270, H.271, K.274 Ligands: TRS.8 Ligand excluded by PLIP TRS.8: 6 residues within 4Å: Chain B: S.119, T.120, Y.269, Y.270, H.271 Ligands: TRS.7 Ligand excluded by PLIP TRS.10: 9 residues within 4Å: Chain C: D.121, L.127, V.129, Y.140, D.171, F.245, H.254, H.271 Ligands: ZN.9 Ligand excluded by PLIP TRS.11: 6 residues within 4Å: Chain C: Y.131, H.257, T.261, H.271, K.274 Ligands: TRS.12 Ligand excluded by PLIP TRS.12: 6 residues within 4Å: Chain C: S.119, T.120, Y.269, Y.270, H.271 Ligands: TRS.11 Ligand excluded by PLIP TRS.14: 8 residues within 4Å: Chain D: D.121, L.127, Y.140, D.171, F.245, H.254, H.271 Ligands: ZN.13 Ligand excluded by PLIP TRS.15: 7 residues within 4Å: Chain D: Y.131, E.136, H.257, T.261, H.271, K.274 Ligands: TRS.16 Ligand excluded by PLIP TRS.16: 5 residues within 4Å: Chain D: G.94, T.120, Y.270, H.271 Ligands: TRS.15 Ligand excluded by PLIP TRS.18: 9 residues within 4Å: Chain E: T.120, D.121, V.129, Y.140, D.171, F.245, H.254, H.271 Ligands: ZN.17 Ligand excluded by PLIP TRS.19: 6 residues within 4Å: Chain E: Y.131, H.257, T.261, H.271, K.274 Ligands: TRS.20 Ligand excluded by PLIP TRS.20: 4 residues within 4Å: Chain E: S.119, Y.270, H.271 Ligands: TRS.19 Ligand excluded by PLIP TRS.22: 9 residues within 4Å: Chain F: D.121, L.127, V.129, Y.140, D.171, F.245, H.254, H.271 Ligands: ZN.21 Ligand excluded by PLIP TRS.23: 9 residues within 4Å: Chain F: Y.131, G.135, H.257, T.261, Y.269, Y.270, H.271, K.274 Ligands: TRS.24 Ligand excluded by PLIP TRS.24: 6 residues within 4Å: Chain F: S.119, T.120, Y.269, Y.270, H.271 Ligands: TRS.23 Ligand excluded by PLIP TRS.26: 9 residues within 4Å: Chain G: D.121, L.127, V.129, Y.140, D.171, F.245, H.254, H.271 Ligands: ZN.25 Ligand excluded by PLIP TRS.27: 6 residues within 4Å: Chain G: Y.131, H.257, T.261, H.271, K.274 Ligands: TRS.28 Ligand excluded by PLIP TRS.28: 6 residues within 4Å: Chain G: S.119, T.120, Y.269, Y.270, H.271 Ligands: TRS.27 Ligand excluded by PLIP TRS.30: 8 residues within 4Å: Chain H: D.121, L.127, Y.140, D.171, F.245, H.254, H.271 Ligands: ZN.29 Ligand excluded by PLIP TRS.31: 7 residues within 4Å: Chain H: Y.131, E.136, H.257, T.261, H.271, K.274 Ligands: TRS.32 Ligand excluded by PLIP TRS.32: 5 residues within 4Å: Chain H: G.94, T.120, Y.270, H.271 Ligands: TRS.31 Ligand excluded by PLIP

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
C

D
D

E
A

F
B

G
C

H
D

Glycerol dehydrogenase

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