SMTL ID : 6n2o.1

2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus with 2-oxoglutarate, coenzyme A and succinyl-CoA bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

hetero-2-2-mer

Ligands

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.1: 12 residues within 4Å: Chain A: I.226, T.227, R.303, T.308, P.311 Chain B: I.58, R.63, H.74, L.135, T.136 Chain C: L.426 Ligands: TPP.4 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.58, B:L.135, A:T.308 Salt bridges: B:R.63, A:R.303 Hydrogen bonds: A:T.227, A:T.227, A:R.303, A:R.303

1 x COA: COENZYME A(Non-covalent)

COA.2: 16 residues within 4Å: Chain A: G.14, G.15, G.17, I.18, I.19, S.20, F.42, R.129, N.132, M.133, K.157, F.158, N.169 Chain B: K.137, Y.151, F.212 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.15, A:G.17, A:I.18, A:I.19, A:S.20, A:N.132, A:N.169, B:K.137 Salt bridges: A:K.157 pi-Stacking: A:F.158, A:F.158 Hydrophobic interactions: B:K.137, B:F.212

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

SF4.3: 11 residues within 4Å: Chain A: I.46 Chain B: W.25, C.26, C.29, H.31, C.60, N.130, C.209, P.210, T.211, F.212 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.26, B:C.29, B:C.60, B:C.209 SF4.7: 11 residues within 4Å: Chain C: I.46 Chain D: W.25, C.26, C.29, H.31, C.60, N.130, C.209, P.210, T.211, F.212 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.26, D:C.29, D:C.60, D:C.209

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 25 residues within 4Å: Chain A: Y.224, P.225, I.226, E.253, P.277 Chain B: H.31, I.58, G.59, C.60, S.61, H.77, G.101, D.102, G.103, D.104, I.108, N.130, I.132, Y.133, G.134, L.135, T.136 Chain C: E.284 Ligands: AKG.1, MG.5 18 PLIP interactions: 3 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:Y.224, A:I.226, A:P.277, B:H.77, B:I.108 Hydrogen bonds: B:C.60, B:S.61, B:D.102, B:G.103, B:D.104, B:N.130, B:G.134, B:L.135 Water bridges: B:D.102, B:D.102 Salt bridges: B:H.31 pi-Cation interactions: B:H.77, B:H.77 TPP.8: 26 residues within 4Å: Chain A: E.284 Chain C: Y.224, P.225, I.226, E.253, L.281, R.303 Chain D: H.31, I.58, G.59, C.60, S.61, H.77, G.101, D.102, G.103, D.104, I.108, N.130, I.132, Y.133, G.134, L.135, T.136 Ligands: SCA.6, MG.9 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:H.77, D:I.108, D:T.136, C:Y.224, C:I.226, C:L.281 Hydrogen bonds: D:C.60, D:S.61, D:G.101, D:D.102, D:G.103, D:D.104, D:G.134, D:L.135, C:R.303 Water bridges: D:N.130 pi-Stacking: D:H.77

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain B: D.102, N.130, I.132 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.102, B:I.132, H2O.1 MG.9: 4 residues within 4Å: Chain D: D.102, N.130, I.132 Ligands: TPP.8 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.102, D:I.132, H2O.1

1 x SCA: SUCCINYL-COENZYME A(Non-covalent)

SCA.6: 34 residues within 4Å: Chain A: L.426 Chain C: G.14, G.15, E.16, G.17, I.18, I.19, S.20, F.42, P.43, A.44, E.45, I.46, A.51, R.129, N.132, M.133, K.157, F.158, K.161, V.165, N.169, T.227, R.303, T.308, P.311, T.312 Chain D: I.58, R.63, H.74, L.135, T.136, K.137 Ligands: TPP.8 24 PLIP interactions: 19 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:T.308, C:T.312, D:I.58, D:L.135 Hydrogen bonds: C:G.15, C:G.17, C:I.18, C:I.19, C:S.20, C:S.20, C:A.44, C:E.45, C:R.129, C:N.132, C:N.169, C:N.169, C:T.227, C:R.303, C:R.303, D:K.137 Salt bridges: C:K.161, D:R.63, D:H.74 pi-Stacking: C:F.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, P.Y. et al., A reverse TCA cycle 2-oxoacid:ferredoxin oxidoreductase that makes C-C bonds from CO2. Joule (2019)

Release Date

2019-03-20

Peptides

Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein: AC
Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein

Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit

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