SMTL ID : 4ylf.1 (1 other biounit)

Insights into flavin-based electron bifurcation via the NADH-dependent reduced ferredoxin-NADP oxidoreductase structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-oligomer

Ligands

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 11 residues within 4Å: Chain A: M.218, V.219, D.220, G.221, G.223, M.224, C.225, G.226, A.227, C.228, C.240 5 PLIP interactions: 5 interactions with chain A, Metal complexes: A:D.220, A:D.220, A:C.225, A:C.228, A:C.240

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 24 residues within 4Å: Chain A: E.48, I.50, P.51, L.52, T.53, V.67, V.68, K.69, V.71, G.72, K.73, T.74, T.75, T.117, L.214, N.215, P.216, I.217, M.218, L.260, Y.263, E.265, Q.266, I.269 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.51 Hydrogen bonds: A:P.51, A:T.53, A:T.53, A:V.67, A:K.69, A:G.72, A:K.73, A:T.74, A:T.75, A:P.216, A:M.218, A:Y.263, A:E.265 Water bridges: A:V.67 FAD.5: 35 residues within 4Å: Chain B: V.89, V.146, G.147, S.148, G.149, P.150, A.151, F.169, E.170, A.171, F.172, G.177, V.178, L.179, Y.181, I.183, R.187, T.211, V.212, V.213, G.232, T.233, G.234, L.258, N.289, T.290, D.293, L.399, G.431, G.432, D.433, A.439, T.440, V.441, A.444 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:V.178, B:V.178, B:I.183, B:L.258, B:T.290 Hydrogen bonds: B:V.89, B:S.148, B:A.151, B:A.171, B:G.177, B:V.178, B:R.187, B:R.187, B:V.213, B:V.213, B:N.289, B:D.433, B:A.439, B:V.441 Water bridges: B:Y.181, B:Y.181, B:G.234, B:D.433, B:I.442

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

SF4.3: 8 residues within 4Å: Chain B: C.39, L.40, C.42, C.47, C.100, V.101, V.111, I.113 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.39, B:C.42, B:C.47, B:C.100 SF4.4: 10 residues within 4Å: Chain B: C.51, P.52, I.55, N.80, C.90, Q.92, Q.95, C.96, E.117, I.442 7 PLIP interactions: 7 interactions with chain B, Salt bridges: B:E.117, B:E.117, B:E.117 Metal complexes: B:C.51, B:C.90, B:C.96, B:E.117

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 8 residues within 4Å: Chain B: Y.73, K.77, N.81, L.82, P.83, A.84, A.121, E.196 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.73, B:N.81, B:A.84 Salt bridges: B:K.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Demmer, J.K. et al., Insights into Flavin-based Electron Bifurcation via the NADH-dependent Reduced Ferredoxin:NADP Oxidoreductase Structure. J.Biol.Chem. (2015)

Release Date

2015-07-08

Peptides

Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog: A
Dihydropyrimidine dehydrogenase subunit A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog

Dihydropyrimidine dehydrogenase subunit A

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