SMTL ID : 1uw8.1

CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 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.16, H2O.16 MN.2: 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.16 MN.4: 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.31, H2O.31 MN.5: 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.31 MN.7: 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.47, H2O.47 MN.8: 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.47 MN.10: 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.62, H2O.62 MN.11: 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.62 MN.13: 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.78, H2O.78 MN.14: 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.78 MN.16: 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.93, H2O.93 MN.17: 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.93

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

TRS.3: 7 residues within 4Å: Chain A: P.276, N.277, H.339, A.341 Chain C: E.117, P.135, S.136 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.136, A:H.339 Water bridges: C:E.117, C:E.117, C:E.117 TRS.6: 7 residues within 4Å: Chain A: E.117, P.135, S.136 Chain B: P.276, N.277, H.339, A.341 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:H.339, A:S.136 Water bridges: A:E.117, A:E.117, A:E.117 TRS.9: 7 residues within 4Å: Chain B: E.117, P.135, S.136 Chain C: P.276, N.277, H.339, A.341 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:H.339, B:S.136 Water bridges: B:E.117, B:E.117, B:E.117 TRS.12: 7 residues within 4Å: Chain D: P.276, N.277, H.339, A.341 Chain F: E.117, P.135, S.136 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:S.136, D:H.339 Water bridges: F:E.117, F:E.117 TRS.15: 7 residues within 4Å: Chain D: E.117, P.135, S.136 Chain E: P.276, N.277, H.339, A.341 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:S.136, E:H.339 Water bridges: D:E.117, D:E.117 TRS.18: 7 residues within 4Å: Chain E: E.117, P.135, S.136 Chain F: P.276, N.277, H.339, A.341 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:H.339, E:S.136 Water bridges: E:E.117, E:E.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Just, V.J. et al., A Closed Conformation of Bacillus Subtilis Oxalate Decarboxylase Oxdc Provides Evidence for the True Identity of the Active Site. J.Biol.Chem. (2004)

Release Date

2004-02-19

Peptides

OXALATE DECARBOXYLASE OXDC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

OXALATE DECARBOXYLASE OXDC

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