SMTL ID : 6ufi.1

W96Y Oxalate Decarboxylase (Bacillus subtilis)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-hexamer

Ligands

12 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: H.273, H.275, E.280, H.319, E.333 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.273, A:H.275, A:E.280, A:H.319, H2O.1 MN.2: 4 residues within 4Å: Chain A: H.95, H.97, E.101, H.140 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.95, A:H.97, A:E.101, A:H.140, H2O.3, H2O.9 MN.7: 5 residues within 4Å: Chain B: H.273, H.275, E.280, H.319, E.333 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.273, B:H.275, B:E.280, B:H.319, H2O.10 MN.8: 4 residues within 4Å: Chain B: H.95, H.97, E.101, H.140 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.95, B:H.97, B:E.101, B:H.140, H2O.13, H2O.18 MN.13: 5 residues within 4Å: Chain C: H.273, H.275, E.280, H.319, E.333 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.273, C:H.275, C:E.280, C:H.319, H2O.20 MN.14: 4 residues within 4Å: Chain C: H.95, H.97, E.101, H.140 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.95, C:H.97, C:E.101, C:H.140, H2O.22, H2O.27 MN.19: 5 residues within 4Å: Chain D: H.273, H.275, E.280, H.319, E.333 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.273, D:H.275, D:E.280, D:H.319, H2O.29 MN.20: 4 residues within 4Å: Chain D: H.95, H.97, E.101, H.140 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.95, D:H.97, D:E.101, D:H.140, H2O.31, H2O.37 MN.25: 5 residues within 4Å: Chain E: H.273, H.275, E.280, H.319, E.333 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.273, E:H.275, E:E.280, E:H.319, H2O.38 MN.26: 4 residues within 4Å: Chain E: H.95, H.97, E.101, H.140 6 PLIP interactions: 4 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.95, E:H.97, E:E.101, E:H.140, H2O.41, H2O.46 MN.31: 5 residues within 4Å: Chain F: H.273, H.275, E.280, H.319, E.333 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.273, F:H.275, F:E.280, F:H.319, H2O.48 MN.32: 4 residues within 4Å: Chain F: H.95, H.97, E.101, H.140 6 PLIP interactions: 4 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.95, F:H.97, F:E.101, F:H.140, H2O.50, H2O.55

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: E.146 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.146, A:E.146 GOL.9: 1 residues within 4Å: Chain B: E.146 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.146, B:E.146 GOL.15: 1 residues within 4Å: Chain C: E.146 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.146, C:E.146 GOL.21: 1 residues within 4Å: Chain D: E.146 2 PLIP interactions: 2 interactions with chain D Water bridges: D:E.146, D:E.146 GOL.27: 1 residues within 4Å: Chain E: E.146 2 PLIP interactions: 2 interactions with chain E Water bridges: E:E.146, E:E.146 GOL.33: 1 residues within 4Å: Chain F: E.146 2 PLIP interactions: 2 interactions with chain F Water bridges: F:E.146, F:E.146

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: K.373 Chain B: V.215 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: K.177, E.178 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: K.373 Chain C: V.215 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: K.177, E.178 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: V.215 Chain C: K.373 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain C: K.177, E.178 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: K.373 Chain E: V.215 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain D: K.177, E.178 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain E: K.373 Chain F: V.215 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain E: K.177, E.178 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain D: V.215 Chain F: K.373 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain F: K.177, E.178 Ligand excluded by PLIP

6 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: V.70, R.71 Chain F: P.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.70 NA.12: 3 residues within 4Å: Chain B: V.70, R.71 Chain E: P.74 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.70 NA.18: 3 residues within 4Å: Chain C: V.70, R.71 Chain D: P.74 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.70 NA.24: 3 residues within 4Å: Chain C: P.74 Chain D: V.70, R.71 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.70 NA.30: 3 residues within 4Å: Chain B: P.74 Chain E: V.70, R.71 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.70 NA.36: 3 residues within 4Å: Chain A: P.74 Chain F: V.70, R.71 1 PLIP interactions: 1 interactions with chain F Water bridges: F:R.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pastore, A.J. et al., Oxalate decarboxylase uses electron hole hopping for catalysis. J.Biol.Chem. (2021)

Release Date

2020-09-30

Peptides

Cupin domain-containing protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Cupin domain-containing protein