SMTL ID : 5exd.2 (1 other biounit)

Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-di-oxido-methyl-TPP (COOM-TPP) intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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: 13 residues within 4Å: Chain B: 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 B, Metal complexes: B:C.261, B:C.264, B:C.267, B:C.300 SF4.3: 10 residues within 4Å: Chain B: R.58 Chain C: 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 C, Metal complexes: C:C.24, C:C.27, C:C.52, C:C.225 SF4.6: 13 residues within 4Å: Chain E: C.271, P.272, D.273, 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 E, Salt bridges: E:D.273 Metal complexes: E:C.271, E:C.290, E:C.293, E:C.296 SF4.7: 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 SF4.8: 11 residues within 4Å: Chain E: R.58 Chain F: T.23, C.24, C.27, P.29, C.52, M.53, 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 TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 23 residues within 4Å: Chain A: Y.28, P.29, I.30, E.59, V.83 Chain C: T.50, G.51, C.52, 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 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.74, C:I.74, C:T.75, C:Y.141, C:T.144, A:I.30 Hydrogen bonds: C:T.50, C:C.52, C:M.53, C:G.109, C:D.110, C:D.110, C:G.111, C:G.112, C:N.138, C:N.138, C:A.142, C:N.143 TPP.9: 24 residues within 4Å: Chain A: E.90 Chain D: Y.28, P.29, I.30, E.59, V.83 Chain F: T.50, G.51, C.52, I.74, T.75, G.109, D.110, G.111, G.112, I.116, Y.136, N.138, S.140, Y.141, A.142, N.143, T.144 Ligands: MG.10 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:I.74, F:T.75, F:I.116, F:T.144, D:I.30 Hydrogen bonds: F:T.50, F:T.50, F:C.52, F:G.109, F:G.111, F:G.112, F:Y.136, F:N.138, F:A.142, F:N.143 Water bridges: F:D.110, F:N.138

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain C: D.110, N.138, S.140 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.110, C:S.140, H2O.1 MG.10: 4 residues within 4Å: Chain F: D.110, N.138, S.140 Ligands: TPP.9 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.110, F:S.140, H2O.1

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
G

D
J

B
H

E
K

C
I

F
L

Oxalate oxidoreductase subunit alpha

Oxalate oxidoreductase subunit delta

Oxalate oxidoreductase subunit beta

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