SMTL ID : 5hi0.1

The Substrate Binding Mode and Chemical Basis of a Reaction Specificity Switch in Oxalate Decarboxylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

12 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: H.95, H.97, E.101, H.140 Ligands: OXL.3 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.1 CO.2: 5 residues within 4Å: Chain A: H.272, H.274, E.279, H.318, E.332 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.272, A:H.274, A:E.279, A:H.318, H2O.1 CO.5: 5 residues within 4Å: Chain B: H.95, H.97, E.101, H.140 Ligands: OXL.7 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.5 CO.6: 5 residues within 4Å: Chain B: H.272, H.274, E.279, H.318, E.332 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.272, B:H.274, B:E.279, B:H.318, H2O.5 CO.9: 5 residues within 4Å: Chain C: H.95, H.97, E.101, H.140 Ligands: OXL.11 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.9 CO.10: 5 residues within 4Å: Chain C: H.272, H.274, E.279, H.318, E.332 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.272, C:H.274, C:E.279, C:H.318, H2O.9 CO.13: 5 residues within 4Å: Chain D: H.95, H.97, E.101, H.140 Ligands: OXL.15 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.13 CO.14: 5 residues within 4Å: Chain D: H.272, H.274, E.279, H.318, E.332 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.272, D:H.274, D:E.279, D:H.318, H2O.13 CO.17: 5 residues within 4Å: Chain E: H.95, H.97, E.101, H.140 Ligands: OXL.19 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.17 CO.18: 5 residues within 4Å: Chain E: H.272, H.274, E.279, H.318, E.332 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.272, E:H.274, E:E.279, E:H.318, H2O.17 CO.21: 5 residues within 4Å: Chain F: H.95, H.97, E.101, H.140 Ligands: OXL.23 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.21 CO.22: 5 residues within 4Å: Chain F: H.272, H.274, E.279, H.318, E.332 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.272, F:H.274, F:E.279, F:H.318, H2O.21

6 x OXL: OXALATE ION(Non-covalent)

OXL.3: 11 residues within 4Å: Chain A: M.84, R.92, H.95, H.97, E.101, H.140, L.153, F.155, T.164, Y.199 Ligands: CO.1 7 PLIP interactions: 7 interactions with chain A Salt bridges: A:R.92, A:R.92, A:H.95, A:H.95, A:H.97, A:H.97, A:H.140 OXL.7: 11 residues within 4Å: Chain B: M.84, R.92, H.95, H.97, E.101, H.140, L.153, F.155, T.164, Y.199 Ligands: CO.5 7 PLIP interactions: 7 interactions with chain B Salt bridges: B:R.92, B:R.92, B:H.95, B:H.95, B:H.97, B:H.97, B:H.140 OXL.11: 11 residues within 4Å: Chain C: M.84, R.92, H.95, H.97, E.101, H.140, L.153, F.155, T.164, Y.199 Ligands: CO.9 7 PLIP interactions: 7 interactions with chain C Salt bridges: C:R.92, C:R.92, C:H.95, C:H.95, C:H.97, C:H.97, C:H.140 OXL.15: 11 residues within 4Å: Chain D: M.84, R.92, H.95, H.97, E.101, H.140, L.153, F.155, T.164, Y.199 Ligands: CO.13 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.164, D:Y.199 Salt bridges: D:R.92, D:R.92, D:H.95, D:H.95, D:H.97, D:H.97, D:H.140 OXL.19: 11 residues within 4Å: Chain E: M.84, R.92, H.95, H.97, E.101, H.140, L.153, F.155, T.164, Y.199 Ligands: CO.17 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:T.164, E:Y.199 Salt bridges: E:R.92, E:R.92, E:H.95, E:H.95, E:H.97, E:H.97, E:H.140 OXL.23: 11 residues within 4Å: Chain F: M.84, R.92, H.95, H.97, E.101, H.140, L.153, F.155, T.164, Y.199 Ligands: CO.21 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:T.164, F:Y.199 Salt bridges: F:R.92, F:R.92, F:H.95, F:H.95, F:H.97, F:H.97, F:H.140

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

NA.4: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.169 NA.8: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.169 NA.12: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.169 NA.16: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.169 NA.20: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain E Water bridges: E:D.169 NA.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, W. et al., Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase. Biochemistry (2016)

Release Date

2016-04-06

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