SMTL ID : 2c3o.1

CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: W.683, C.688, I.689, Q.690, C.691, N.692, Q.693, C.694, C.754, P.755, P.756, A.760, L.761 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.688, A:C.691, A:C.694, A:C.754 SF4.2: 12 residues within 4Å: Chain A: P.681, C.698, P.699, A.702, I.703, C.744, M.745, G.746, C.747, G.748, N.749, C.750 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.698, A:C.744, A:C.747, A:C.750 SF4.3: 11 residues within 4Å: Chain A: K.458, A.810, C.811, C.814, E.816, C.839, W.843, S.994, C.1070, I.1071 Chain B: M.1202 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A, Salt bridges: B:D.1197, A:E.816 Metal complexes: A:C.811, A:C.814, A:C.839, A:C.1070 SF4.8: 13 residues within 4Å: Chain B: W.683, C.688, I.689, Q.690, C.691, N.692, C.694, I.737, C.754, P.755, P.756, A.760, L.761 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.688, B:C.691, B:C.694, B:C.754 SF4.9: 13 residues within 4Å: Chain B: P.681, C.698, P.699, A.702, I.703, C.744, M.745, G.746, C.747, G.748, N.749, C.750, M.763 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.698, B:C.744, B:C.747, B:C.750 SF4.10: 9 residues within 4Å: Chain B: K.458, A.810, C.811, C.814, E.816, C.839, S.994, C.1070, I.1071 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B, Salt bridges: A:D.1197, B:E.816 Metal complexes: B:C.811, B:C.814, B:C.839, B:C.1070

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 25 residues within 4Å: Chain A: Y.27, P.28, I.29, E.63, Q.87, G.88, L.91, E.816, T.837, G.838, C.839, F.868, E.869, G.961, D.962, G.963, W.964, T.990, V.992, Y.993, S.994, N.995, T.996 Ligands: MG.5, PYR.7 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:P.28, A:I.29, A:Q.87, A:L.91, A:F.868, A:T.996 Hydrogen bonds: A:C.839, A:G.961, A:D.962, A:G.963, A:W.964, A:S.994, A:N.995 Water bridges: A:T.837, A:S.840, A:S.840, A:F.868, A:F.868, A:D.962, A:D.962 pi-Stacking: A:F.868 TPP.11: 26 residues within 4Å: Chain B: Y.27, P.28, I.29, E.63, Q.87, G.88, L.91, E.816, T.837, G.838, C.839, F.868, E.869, G.961, D.962, G.963, W.964, I.968, T.990, V.992, Y.993, S.994, N.995, T.996 Ligands: MG.12, PYR.14 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:P.28, B:I.29, B:Q.87, B:L.91, B:F.868, B:I.968, B:Y.993, B:Y.993, B:T.996 Hydrogen bonds: B:C.839, B:G.961, B:G.963, B:W.964, B:T.990, B:S.994, B:N.995 Water bridges: B:S.840, B:S.840, B:F.868, B:F.868, B:D.962, B:D.962 pi-Stacking: B:F.868

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: D.962, T.990, V.992, Y.993, S.994 Ligands: TPP.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.962, A:T.990, A:V.992, H2O.9 MG.12: 5 residues within 4Å: Chain B: D.962, G.963, T.990, V.992 Ligands: TPP.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.962, B:T.990, B:V.992, H2O.20

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 8 residues within 4Å: Chain A: D.982, V.983, N.984, A.1055, E.1056, F.1058, G.1060, S.1062 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.982, A:F.1058, A:G.1060 CA.13: 7 residues within 4Å: Chain B: D.982, N.984, A.1055, E.1056, F.1058, G.1060, S.1062 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.982, B:A.1055, B:F.1058, B:G.1060

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.7: 10 residues within 4Å: Chain A: I.29, T.30, R.113, L.120, I.122, I.842, N.995, T.996 Chain B: M.1201 Ligands: TPP.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.842 Hydrogen bonds: A:T.30, A:R.113, A:R.113 Salt bridges: A:R.113 PYR.14: 9 residues within 4Å: Chain A: M.1201 Chain B: I.29, T.30, R.113, I.122, T.837, N.995, T.996 Ligands: TPP.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:T.837 Hydrogen bonds: B:T.30, B:T.30, B:R.113, B:R.113, B:N.995 Salt bridges: B:R.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cavazza, C. et al., Flexibility of Thiamine Diphosphate Revealed by Kinetic Crystallographic Studies of the Reaction of Pyruvate-Ferredoxin Oxidoreductase with Pyruvate. Structure (2006)

Release Date

2006-02-15

Peptides

PYRUVATE-FERREDOXIN OXIDOREDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PYRUVATE-FERREDOXIN OXIDOREDUCTASE

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