SMTL ID : 2uya.1

DEL162-163 mutant of Bacillus subtilis Oxalate Decarboxylase OxdC

Coordinates

PDB Format

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.271, H.273, E.278, H.317, E.331 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.271, A:H.273, A:E.278, A:H.317, H2O.16 MN.6: 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.32, H2O.32 MN.7: 5 residues within 4Å: Chain B: H.271, H.273, E.278, H.317, E.331 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.271, B:H.273, B:E.278, B:H.317, H2O.32 MN.11: 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.48, H2O.48 MN.12: 5 residues within 4Å: Chain C: H.271, H.273, E.278, H.317, E.331 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.271, C:H.273, C:E.278, C:H.317, H2O.48 MN.16: 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.63, H2O.64 MN.17: 5 residues within 4Å: Chain D: H.271, H.273, E.278, H.317, E.331 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.271, D:H.273, D:E.278, D:H.317, H2O.64 MN.21: 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.79, H2O.79 MN.22: 5 residues within 4Å: Chain E: H.271, H.273, E.278, H.317, E.331 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.271, E:H.273, E:E.278, E:H.317, H2O.79 MN.26: 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.95, H2O.95 MN.27: 5 residues within 4Å: Chain F: H.271, H.273, E.278, H.317, E.331 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.271, F:H.273, F:E.278, F:H.317, H2O.95

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

TRS.3: 7 residues within 4Å: Chain A: P.274, N.275, H.337, A.339 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.337 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.274, N.275, H.337, A.339 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.136, B:H.337 Water bridges: A:E.117, A:E.117 TRS.13: 7 residues within 4Å: Chain B: E.117, P.135, S.136 Chain C: P.274, N.275, H.337, A.339 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:H.337, B:S.136 Water bridges: B:E.117, B:E.117 TRS.18: 7 residues within 4Å: Chain D: P.274, N.275, H.337, A.339 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.337, F:S.136 Water bridges: F:E.117, F:E.117 TRS.23: 7 residues within 4Å: Chain D: E.117, P.135, S.136 Chain E: P.274, N.275, H.337, A.339 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:S.136, E:H.337 Water bridges: D:E.117, D:E.117 TRS.28: 7 residues within 4Å: Chain E: E.117, P.135, S.136 Chain F: P.274, N.275, H.337, A.339 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:S.136, F:H.337 Water bridges: E:E.117, E:E.117

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: H.56, R.58 Chain D: H.42, G.43, T.44 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:H.56, D:G.43 Water bridges: A:R.58, D:G.43, D:T.44 GOL.9: 5 residues within 4Å: Chain B: H.56, R.58 Chain F: H.42, G.43, T.44 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:H.56, F:G.43 Water bridges: B:R.58, F:G.43, F:T.44 GOL.14: 5 residues within 4Å: Chain C: H.56, R.58 Chain E: H.42, G.43, T.44 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.43, C:H.56 Water bridges: E:G.43, E:T.44, C:R.58 GOL.19: 5 residues within 4Å: Chain A: H.42, G.43, T.44 Chain D: H.56, R.58 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:H.56, A:G.43 Water bridges: D:R.58, A:G.43, A:T.44 GOL.24: 5 residues within 4Å: Chain C: H.42, G.43, T.44 Chain E: H.56, R.58 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:G.43, E:H.56 Water bridges: C:G.43, C:T.44, E:R.58 GOL.29: 5 residues within 4Å: Chain B: H.42, G.43, T.44 Chain F: H.56, R.58 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:G.43, F:H.56 Water bridges: B:G.43, B:T.44, F:R.58

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

CL.5: 2 residues within 4Å: Chain A: M.84, R.92 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: M.84, R.92 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: M.84, R.92 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain D: M.84, R.92 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain E: M.84, R.92 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain F: M.84, R.92 Ligand excluded by PLIP

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