SMTL ID : 5b47.1

2-Oxoacid:Ferredoxin Oxidoreductase 2 from Sulfolobus tokodai - pyruvate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 9 residues within 4Å: Chain A: S.42, I.256, T.257, R.344, T.349, P.352 Chain B: I.44, L.123 Ligands: TPP.3 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.349, A:P.352, B:I.44, B:L.123 Hydrogen bonds: A:T.257, A:R.344, A:R.344 Salt bridges: A:R.344 PYR.5: 9 residues within 4Å: Chain C: S.42, I.256, T.257, R.344, T.349, P.352 Chain D: I.44, L.123 Ligands: TPP.7 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:T.349, C:P.352, D:I.44, D:L.123 Hydrogen bonds: C:T.257, C:R.344, C:R.344 Salt bridges: C:R.344

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

SF4.2: 8 residues within 4Å: Chain A: I.44 Chain B: W.11, C.12, C.15, C.46, N.118, C.197, T.199 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:D.17 Metal complexes: B:C.12, B:C.15, B:C.46, B:C.197 SF4.6: 8 residues within 4Å: Chain C: I.44 Chain D: W.11, C.12, C.15, C.46, N.118, C.197, T.199 5 PLIP interactions: 5 interactions with chain D, Salt bridges: D:D.17 Metal complexes: D:C.12, D:C.15, D:C.46, D:C.197

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 24 residues within 4Å: Chain A: Y.254, P.255, I.256, E.294, P.318, L.322, R.344 Chain B: I.44, G.45, C.46, S.47, H.65, G.89, D.90, G.91, D.92, N.118, V.120, Y.121, G.122, L.123 Chain C: E.325 Ligands: PYR.1, MG.4 18 PLIP interactions: 6 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:Y.254, A:P.255, A:I.256, A:P.318, A:L.322 Hydrogen bonds: A:R.344, B:C.46, B:S.47, B:S.47, B:D.90, B:G.91, B:D.92, B:N.118, B:G.122, B:L.123 Salt bridges: B:H.65 pi-Stacking: B:H.65 pi-Cation interactions: B:H.65 TPP.7: 24 residues within 4Å: Chain A: E.325 Chain C: Y.254, P.255, I.256, E.294, P.318, L.322, R.344 Chain D: I.44, G.45, C.46, S.47, H.65, G.89, D.90, G.91, D.92, N.118, V.120, Y.121, G.122, L.123 Ligands: PYR.5, MG.8 18 PLIP interactions: 12 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:C.46, D:S.47, D:S.47, D:D.90, D:G.91, D:D.92, D:N.118, D:G.122, D:L.123, C:R.344 Salt bridges: D:H.65 pi-Stacking: D:H.65 pi-Cation interactions: D:H.65 Hydrophobic interactions: C:Y.254, C:P.255, C:I.256, C:P.318, C:L.322

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain B: G.89, D.90, H.116, N.118, V.120 Ligands: TPP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.90 MG.8: 6 residues within 4Å: Chain D: G.89, D.90, H.116, N.118, V.120 Ligands: TPP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, Z. et al., Crystal structures of archaeal 2-oxoacid:ferredoxin oxidoreductases from Sulfolobus tokodaii. Sci Rep (2016)

Release Date

2016-09-28

Peptides

2-oxoacid--ferredoxin oxidoreductase alpha subunit: AC
2-oxoacid--ferredoxin oxidoreductase beta subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

2-oxoacid--ferredoxin oxidoreductase alpha subunit

2-oxoacid--ferredoxin oxidoreductase beta subunit

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