SMTL ID : 7y9p.1

Xylitol dehydrogenase S96C/S99C/Y102C mutant(thermostabilized form) from Pichia stipitis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.52, H.77, E.78, E.170 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.52, A:H.77, A:E.78, H2O.1 ZN.2: 5 residues within 4Å: Chain A: C.107, R.108, C.110, C.113, C.121 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.113, A:C.121 ZN.6: 4 residues within 4Å: Chain B: C.52, H.77, E.78, E.170 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.52, B:H.77, B:E.78, H2O.1 ZN.7: 5 residues within 4Å: Chain B: C.107, R.108, C.110, C.113, C.121 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.107, B:C.110, B:C.113, B:C.121 ZN.11: 4 residues within 4Å: Chain C: C.52, H.77, E.78, E.170 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.52, C:H.77, C:E.78, H2O.2 ZN.12: 5 residues within 4Å: Chain C: C.107, R.108, C.110, C.113, C.121 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.107, C:C.110, C:C.113, C:C.121 ZN.16: 4 residues within 4Å: Chain D: C.52, H.77, E.78, E.170 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.52, D:H.77, D:E.78, H2O.3 ZN.17: 5 residues within 4Å: Chain D: C.107, R.108, C.110, C.113, C.121 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.107, D:C.110, D:C.113, D:C.121

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: D.111, E.112, S.115, H.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.112 GOL.8: 4 residues within 4Å: Chain B: D.111, E.112, S.115, H.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.112 GOL.13: 4 residues within 4Å: Chain C: D.111, E.112, S.115, H.117 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.112 GOL.18: 4 residues within 4Å: Chain D: D.111, E.112, S.115, H.117 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.112

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: I.219, F.220, D.221, N.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.221, A:D.221, A:N.222, A:N.222 SO4.9: 4 residues within 4Å: Chain B: I.219, F.220, D.221, N.222 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.221, B:D.221, B:N.222, B:N.222 SO4.14: 4 residues within 4Å: Chain C: I.219, F.220, D.221, N.222 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.221, C:N.222, C:N.222 SO4.19: 4 residues within 4Å: Chain D: I.219, F.220, D.221, N.222 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.221, D:N.222, D:N.222

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

PEG.5: 8 residues within 4Å: Chain A: C.52, G.53, G.194, G.196, P.197, V.198, G.199, C.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.53, A:G.196, A:V.198 Water bridges: A:A.195 PEG.10: 8 residues within 4Å: Chain B: C.52, G.53, G.194, G.196, P.197, V.198, G.199, C.262 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.53, B:G.196, B:V.198 Water bridges: B:A.195 PEG.15: 8 residues within 4Å: Chain C: C.52, G.53, G.194, G.196, P.197, V.198, G.199, C.262 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.53, C:G.196, C:V.198 Water bridges: C:A.195 PEG.20: 8 residues within 4Å: Chain D: C.52, G.53, G.194, G.196, P.197, V.198, G.199, C.262 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.53, D:G.196, D:V.198 Water bridges: D:A.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshiwara, K. et al., Molecular evolutionary insight of structural zinc atom in yeast xylitol dehydrogenases and its application in bioethanol production by lignocellulosic biomass. Sci Rep (2023)

Release Date

2023-02-15

Peptides

Xylitol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Xylitol dehydrogenase