SMTL ID : 5exe.1

Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-TPP adduct

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-2-2-2-mer

Ligands

6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain B: P.254, C.271, C.275, I.276, F.285, C.290, K.291, G.292, C.293, G.294, L.295, C.296 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:D.273 Metal complexes: B:C.271, B:C.290, B:C.293, B:C.296 SF4.2: 12 residues within 4Å: Chain B: I.256, C.261, T.262, E.263, C.264, Y.265, T.266, C.267, C.300, P.301, S.302, L.305 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.261, B:C.264, B:C.267, B:C.300 SF4.3: 9 residues within 4Å: Chain B: R.58 Chain C: C.24, C.27, P.29, C.52, N.138, C.225, P.226, K.227 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.24, C:C.27, C:C.52, C:C.225 SF4.7: 11 residues within 4Å: Chain E: P.254, C.271, I.276, F.285, C.290, K.291, G.292, C.293, G.294, L.295, C.296 5 PLIP interactions: 5 interactions with chain E, Salt bridges: E:D.273 Metal complexes: E:C.271, E:C.290, E:C.293, E:C.296 SF4.8: 13 residues within 4Å: Chain E: I.256, C.261, T.262, E.263, C.264, Y.265, T.266, C.267, P.283, C.300, P.301, S.302, L.305 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.261, E:C.264, E:C.267, E:C.300 SF4.9: 10 residues within 4Å: Chain E: R.58 Chain F: T.23, C.24, C.27, P.29, C.52, N.138, C.225, P.226, K.227 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.24, F:C.27, F:C.52, F:C.225

2 x 5SR: [2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-carboxy-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-oxidanyl-phosphoryl] hydrogen phosphate(Non-covalent)

5SR.4: 26 residues within 4Å: Chain A: Y.28, P.29, I.30, E.59, V.83, R.109, F.117 Chain C: T.50, G.51, C.52, V.55, I.74, T.75, G.109, D.110, G.111, G.112, Y.136, N.138, S.140, Y.141, A.142, N.143, T.144 Chain D: E.90 Ligands: MG.5 23 PLIP interactions: 19 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:I.74, C:T.75, C:T.144, A:I.30 Hydrogen bonds: C:T.50, C:T.50, C:C.52, C:G.109, C:D.110, C:G.111, C:G.112, C:N.138, C:S.140, C:A.142, C:N.143, C:N.143 Water bridges: C:Q.73, C:I.74, C:N.138, C:N.138, A:R.31, A:R.109 Salt bridges: A:R.109 5SR.10: 26 residues within 4Å: Chain A: E.90 Chain D: Y.28, P.29, I.30, E.59, V.83, R.109, D.116 Chain F: T.50, G.51, C.52, V.55, I.74, T.75, G.109, D.110, G.111, G.112, Y.136, N.138, S.140, Y.141, A.142, N.143, T.144 Ligands: MG.11 24 PLIP interactions: 20 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: F:I.74, F:T.75, F:T.144, D:I.30 Hydrogen bonds: F:T.50, F:T.50, F:C.52, F:G.109, F:D.110, F:G.111, F:G.112, F:Y.136, F:N.138, F:S.140, F:A.142, F:N.143, F:N.143 Water bridges: F:Q.73, F:I.74, F:N.138, F:N.138, D:R.109, D:R.109 Salt bridges: D:R.109

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain C: D.110, N.138, S.140 Ligands: 5SR.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.110, C:S.140, H2O.37 MG.6: 4 residues within 4Å: Chain C: D.130, G.210, L.211, Q.213 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.130, C:L.211, C:Q.213, H2O.36, H2O.36 MG.11: 4 residues within 4Å: Chain F: D.110, N.138, S.140 Ligands: 5SR.10 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.110, F:S.140, H2O.82

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

NA.12: 3 residues within 4Å: Chain F: D.130, L.211, Q.213 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gibson, M.I. et al., One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2015-12-30

Peptides

Oxalate oxidoreductase subunit alpha: AD
Oxalate oxidoreductase subunit delta: BE
Oxalate oxidoreductase subunit beta: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Oxalate oxidoreductase subunit alpha

Oxalate oxidoreductase subunit delta

Oxalate oxidoreductase subunit beta

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