SMTL ID : 7plm.1

CryoEM reconstruction of pyruvate ferredoxin oxidoreductase (PFOR) in anaerobic conditions

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: W.684, C.689, I.690, Q.691, C.692, N.693, C.695, I.738, C.755, P.756, P.757, A.761, L.762 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.689, A:C.692, A:C.695, A:C.755 SF4.2: 13 residues within 4Å: Chain A: P.682, C.699, P.700, A.703, I.704, C.745, M.746, G.747, C.748, G.749, N.750, C.751, M.764 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.699, A:C.745, A:C.748, A:C.751 SF4.3: 11 residues within 4Å: Chain A: K.459, A.811, C.812, C.815, E.817, C.840, W.844, S.995, C.1071, I.1072 Chain B: D.1198 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, Salt bridges: A:E.817, B:D.1198 Metal complexes: A:C.812, A:C.815, A:C.840, A:C.1071 SF4.7: 13 residues within 4Å: Chain B: W.684, C.689, I.690, Q.691, C.692, N.693, C.695, I.738, C.755, P.756, P.757, A.761, L.762 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.689, B:C.692, B:C.695, B:C.755 SF4.8: 13 residues within 4Å: Chain B: P.682, C.699, P.700, A.703, I.704, C.745, M.746, G.747, C.748, G.749, N.750, C.751, M.764 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.699, B:C.745, B:C.748, B:C.751 SF4.9: 11 residues within 4Å: Chain A: D.1198 Chain B: K.459, A.811, C.812, C.815, E.817, C.840, W.844, S.995, C.1071, I.1072 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A, Salt bridges: B:E.817, A:D.1198 Metal complexes: B:C.812, B:C.815, B:C.840, B:C.1071

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 23 residues within 4Å: Chain A: Y.28, P.29, I.30, E.64, Q.88, L.92, E.817, T.838, G.839, C.840, F.869, G.962, D.963, G.964, W.965, I.969, T.991, V.993, Y.994, S.995, N.996, T.997 Ligands: MG.6 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.28, A:I.30, A:L.92, A:F.869, A:F.869, A:I.969, A:Y.994, A:T.997 Hydrogen bonds: A:E.817, A:C.840, A:G.962, A:D.963, A:G.964, A:W.965, A:T.991, A:S.995, A:N.996 Water bridges: A:T.838, A:T.838, A:T.991 pi-Stacking: A:F.869 TPP.10: 23 residues within 4Å: Chain B: Y.28, P.29, I.30, E.64, Q.88, L.92, E.817, T.838, G.839, C.840, F.869, G.962, D.963, G.964, W.965, I.969, T.991, V.993, Y.994, S.995, N.996, T.997 Ligands: MG.12 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.28, B:I.30, B:L.92, B:F.869, B:F.869, B:I.969, B:Y.994, B:T.997 Hydrogen bonds: B:E.817, B:C.840, B:G.962, B:D.963, B:G.964, B:W.965, B:T.991, B:S.995, B:N.996 Water bridges: B:T.838, B:T.838, B:T.991 pi-Stacking: B:F.869

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.983, N.985, A.1056, F.1059, G.1061 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.983, A:F.1059, A:G.1061 CA.11: 5 residues within 4Å: Chain B: D.983, N.985, A.1056, F.1059, G.1061 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.983, B:F.1059, B:G.1061

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: D.963, T.991, V.993, S.995 Ligands: TPP.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.963, A:D.963, A:T.991, A:V.993 MG.12: 5 residues within 4Å: Chain B: D.963, T.991, V.993, S.995 Ligands: TPP.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.963, B:D.963, B:T.991, B:V.993

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cherrier, M.V. et al., Oxygen-Sensitive Metalloprotein Structure Determination by Cryo-Electron Microscopy. Biomolecules (2022)

Release Date

2022-03-23

Peptides

Pyruvate:ferredoxin oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyruvate:ferredoxin oxidoreductase