SMTL ID : 1l3j.1

Crystal Structure of Oxalate Decarboxylase Formate Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.95, H.97, E.101, H.140 Ligands: FMT.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.95, A:H.97, A:E.101, A:H.140 MN.2: 5 residues within 4Å: Chain A: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.273, A:H.275, A:E.280, A:H.319, H2O.241, H2O.245 MN.6: 5 residues within 4Å: Chain B: H.95, H.97, E.101, H.140 Ligands: FMT.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.95, B:H.97, B:E.101, B:H.140 MN.7: 5 residues within 4Å: Chain B: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.273, B:H.275, B:E.280, B:H.319, H2O.625, H2O.629 MN.11: 5 residues within 4Å: Chain C: H.95, H.97, E.101, H.140 Ligands: FMT.14 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.95, C:H.97, C:E.101, C:H.140 MN.12: 5 residues within 4Å: Chain C: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.273, C:H.275, C:E.280, C:H.319, H2O.1009, H2O.1013 MN.16: 5 residues within 4Å: Chain D: H.95, H.97, E.101, H.140 Ligands: FMT.19 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.95, D:H.97, D:E.101, D:H.140 MN.17: 5 residues within 4Å: Chain D: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.273, D:H.275, D:E.280, D:H.319, H2O.1393, H2O.1397 MN.21: 5 residues within 4Å: Chain E: H.95, H.97, E.101, H.140 Ligands: FMT.24 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.95, E:H.97, E:E.101, E:H.140 MN.22: 5 residues within 4Å: Chain E: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.273, E:H.275, E:E.280, E:H.319, H2O.1777, H2O.1781 MN.26: 5 residues within 4Å: Chain F: H.95, H.97, E.101, H.140 Ligands: FMT.29 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.95, F:H.97, F:E.101, F:H.140 MN.27: 5 residues within 4Å: Chain F: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.273, F:H.275, F:E.280, F:H.319, H2O.2161, H2O.2165

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: H.174 Chain B: H.42, G.298 Ligands: FMT.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.174, H2O.383, H2O.384 MG.8: 4 residues within 4Å: Chain B: H.174 Chain C: H.42, G.298 Ligands: FMT.10 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.174, H2O.767, H2O.768 MG.13: 4 residues within 4Å: Chain A: H.42, G.298 Chain C: H.174 Ligands: FMT.15 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.174, H2O.1151, H2O.1152 MG.18: 4 residues within 4Å: Chain D: H.174 Chain E: H.42, G.298 Ligands: FMT.20 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.174, H2O.1535, H2O.1536 MG.23: 4 residues within 4Å: Chain E: H.174 Chain F: H.42, G.298 Ligands: FMT.25 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.174, H2O.1919, H2O.1920 MG.28: 4 residues within 4Å: Chain D: H.42, G.298 Chain F: H.174 Ligands: FMT.30 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.174, H2O.2303, H2O.2304

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

FMT.4: 8 residues within 4Å: Chain A: M.84, R.92, H.95, H.97, E.101, L.153, F.155 Ligands: MN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.92, A:R.92 FMT.5: 5 residues within 4Å: Chain A: A.173, H.174 Chain B: E.39, T.40 Ligands: MG.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.173 FMT.9: 8 residues within 4Å: Chain B: M.84, R.92, H.95, H.97, E.101, L.153, F.155 Ligands: MN.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.92, B:R.92 FMT.10: 5 residues within 4Å: Chain B: A.173, H.174 Chain C: E.39, T.40 Ligands: MG.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.173 FMT.14: 8 residues within 4Å: Chain C: M.84, R.92, H.95, H.97, E.101, L.153, F.155 Ligands: MN.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.92, C:R.92 FMT.15: 5 residues within 4Å: Chain A: E.39, T.40 Chain C: A.173, H.174 Ligands: MG.13 1 PLIP interactions: 1 interactions with chain C Water bridges: C:A.173 FMT.19: 8 residues within 4Å: Chain D: M.84, R.92, H.95, H.97, E.101, L.153, F.155 Ligands: MN.16 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.92, D:R.92 Water bridges: D:Y.200 FMT.20: 5 residues within 4Å: Chain D: A.173, H.174 Chain E: E.39, T.40 Ligands: MG.18 1 PLIP interactions: 1 interactions with chain D Water bridges: D:A.173 FMT.24: 8 residues within 4Å: Chain E: M.84, R.92, H.95, H.97, E.101, L.153, F.155 Ligands: MN.21 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.92, E:R.92 Water bridges: E:Y.200 FMT.25: 5 residues within 4Å: Chain E: A.173, H.174 Chain F: E.39, T.40 Ligands: MG.23 1 PLIP interactions: 1 interactions with chain E Water bridges: E:A.173 FMT.29: 8 residues within 4Å: Chain F: M.84, R.92, H.95, H.97, E.101, L.153, F.155 Ligands: MN.26 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.92, F:R.92 Water bridges: F:Y.200 FMT.30: 5 residues within 4Å: Chain D: E.39, T.40 Chain F: A.173, H.174 Ligands: MG.28 1 PLIP interactions: 1 interactions with chain F Water bridges: F:A.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anand, R. et al., Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution. Biochemistry (2002)

Release Date

2002-07-03

Peptides

YVRK PROTEIN: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

YVRK PROTEIN

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