SMTL ID : 2uyb.1

S161A mutant of Bacillus subtilis Oxalate Decarboxylase OxdC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 9 residues within 4Å: Chain A: M.84, R.92, H.95, H.97, E.101, L.153, F.155, E.162 Ligands: MN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.92 FMT.5: 9 residues within 4Å: Chain B: M.84, R.92, H.95, H.97, E.101, L.153, F.155, E.162 Ligands: MN.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.92 FMT.9: 9 residues within 4Å: Chain C: M.84, R.92, H.95, H.97, E.101, L.153, F.155, E.162 Ligands: MN.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.92 FMT.13: 9 residues within 4Å: Chain D: M.84, R.92, H.95, H.97, E.101, L.153, F.155, E.162 Ligands: MN.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.92 FMT.17: 9 residues within 4Å: Chain E: M.84, R.92, H.95, H.97, E.101, L.153, F.155, E.162 Ligands: MN.18 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.92 FMT.21: 9 residues within 4Å: Chain F: M.84, R.92, H.95, H.97, E.101, L.153, F.155, E.162 Ligands: MN.22 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.92

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

MN.2: 5 residues within 4Å: Chain A: H.95, H.97, E.101, H.140 Ligands: FMT.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.95, A:H.97, A:E.101, A:H.140, H2O.16 MN.3: 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.6: 5 residues within 4Å: Chain B: H.95, H.97, E.101, H.140 Ligands: FMT.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.95, B:H.97, B:E.101, B:H.140, H2O.32 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.32 MN.10: 5 residues within 4Å: Chain C: H.95, H.97, E.101, H.140 Ligands: FMT.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.95, C:H.97, C:E.101, C:H.140, H2O.48 MN.11: 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.48 MN.14: 5 residues within 4Å: Chain D: H.95, H.97, E.101, H.140 Ligands: FMT.13 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.95, D:H.97, D:E.101, D:H.140, H2O.64 MN.15: 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.64 MN.18: 5 residues within 4Å: Chain E: H.95, H.97, E.101, H.140 Ligands: FMT.17 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.95, E:H.97, E:E.101, E:H.140, H2O.80 MN.19: 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.80 MN.22: 5 residues within 4Å: Chain F: H.95, H.97, E.101, H.140 Ligands: FMT.21 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.95, F:H.97, F:E.101, F:H.140, H2O.95 MN.23: 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.95

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

TRS.4: 7 residues within 4Å: Chain A: P.276, N.277, H.339, A.341 Chain C: E.117, P.135, S.136 4 PLIP interactions: 3 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 TRS.8: 7 residues within 4Å: Chain A: E.117, P.135, S.136 Chain B: P.276, N.277, H.339, A.341 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.136, B:H.339 Water bridges: A:E.117, A:E.117 TRS.12: 7 residues within 4Å: Chain B: E.117, P.135, S.136 Chain C: P.276, N.277, H.339, A.341 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.136, C:H.339 Water bridges: B:E.117, B:E.117 TRS.16: 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: 1 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:H.339, F:S.136 Water bridges: F:E.117, F:E.117 TRS.20: 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: 1 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:H.339, D:S.136 Water bridges: D:E.117, D:E.117 TRS.24: 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: 3 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:S.136, F:H.339 Water bridges: E:E.117, E:E.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Just, V.J. et al., The Identity of the Active Site of Oxalate Decarboxylase and the Importance of the Stability of Active-Site Lid Conformations. Biochem.J. (2007)

Release Date

2007-08-21

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