SMTL ID : 6cio.3 (2 other biounits)

Pyruvate:ferredoxin oxidoreductase from Moorella thermoacetica with lactyl-TPP bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: W.681, C.686, I.687, Q.688, C.689, N.690, C.692, C.752, P.753, A.758, L.759 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.686, A:C.689, A:C.692, A:C.752 SF4.2: 10 residues within 4Å: Chain A: P.679, C.696, I.701, C.742, T.743, G.744, C.745, G.746, N.747, C.748 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.696, A:C.742, A:C.745, A:C.748 SF4.3: 11 residues within 4Å: Chain A: K.456, C.809, C.812, E.814, C.837, T.995, S.999, C.1075, I.1076, N.1077, M.1082 6 PLIP interactions: 6 interactions with chain A, Salt bridges: A:E.814, A:E.814 Metal complexes: A:C.809, A:C.812, A:C.837, A:C.1075 SF4.7: 11 residues within 4Å: Chain B: W.681, C.686, I.687, Q.688, C.689, N.690, C.692, I.735, C.752, A.758, L.759 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.686, B:C.689, B:C.692, B:C.752 SF4.8: 12 residues within 4Å: Chain B: P.679, C.696, P.697, A.700, I.701, V.737, C.742, T.743, G.744, C.745, G.746, C.748 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.696, B:C.742, B:C.745, B:C.748 SF4.9: 11 residues within 4Å: Chain B: K.456, A.808, C.809, C.812, E.814, C.837, W.841, S.999, C.1075, I.1076, M.1082 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:E.814 Metal complexes: B:C.809, B:C.812, B:C.837, B:C.1075

1 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 25 residues within 4Å: Chain A: Y.26, P.27, I.28, E.62, Q.86, L.90, R.112, E.814, T.835, G.836, C.837, F.866, E.867, G.966, D.967, G.968, W.969, I.973, T.995, V.997, Y.998, S.999, N.1000, T.1001 Ligands: MG.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.28, A:Q.86, A:L.90, A:F.866, A:I.973, A:Y.998, A:Y.998 Hydrogen bonds: A:R.112, A:C.837, A:D.967, A:G.968, A:W.969, A:T.995, A:V.997, A:S.999, A:N.1000 Water bridges: A:E.814, A:E.814 pi-Stacking: A:F.866

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: D.967, T.995, V.997, S.999 Ligands: TPP.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.967, A:T.995, A:V.997, H2O.1 MG.11: 5 residues within 4Å: Chain B: D.967, T.995, V.997, S.999 Ligands: TDL.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.967, B:T.995, B:V.997, H2O.1

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 6 residues within 4Å: Chain A: S.424, D.425, G.426, T.427, V.428, G.429 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.424, A:S.424, A:D.425, A:G.426, A:T.427, A:V.428, A:G.429 SO4.12: 6 residues within 4Å: Chain B: S.424, D.425, G.426, T.427, V.428, G.429 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.424, B:D.425, B:G.426, B:V.428, B:G.429

1 x TDL: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-CARBOXY-1-HYDROXYETHYL)-5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM(Non-covalent)

TDL.10: 26 residues within 4Å: Chain B: P.27, I.28, T.29, E.62, Q.86, L.90, R.112, I.121, E.814, T.835, G.836, C.837, F.866, E.867, G.966, D.967, G.968, W.969, I.973, T.995, V.997, Y.998, S.999, N.1000, T.1001 Ligands: MG.11 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:I.28, B:Q.86, B:L.90, B:T.835, B:F.866, B:F.866, B:F.866, B:I.973, B:Y.998, B:Y.998 Hydrogen bonds: B:T.29, B:T.29, B:R.112, B:R.112, B:C.837, B:G.966, B:G.968, B:W.969, B:T.995, B:S.999, B:S.999, B:N.1000, B:N.1000 Water bridges: B:E.814, B:D.967 Salt bridges: B:R.112 pi-Stacking: B:F.866

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, P.Y. et al., Binding site for coenzyme A revealed in the structure of pyruvate:ferredoxin oxidoreductase fromMoorella thermoacetica. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-03-28

Peptides

PYRUVATE-FERREDOXIN OXIDOREDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

PYRUVATE-FERREDOXIN OXIDOREDUCTASE

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