SMTL ID : 5jfc.2 (1 other biounit)

NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) from Pyrococcus furiosus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: C.56, P.57, I.60, T.97, C.101, Q.103, Q.106, C.107, I.122, E.126, I.453 7 PLIP interactions: 7 interactions with chain A, Salt bridges: A:E.126, A:E.126, A:E.126 Metal complexes: A:C.56, A:C.101, A:C.107, A:E.126 SF4.2: 7 residues within 4Å: Chain A: C.42, L.43, C.45, C.52, C.111, V.112, I.120 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.42, A:C.45, A:C.52, A:C.111 SF4.7: 11 residues within 4Å: Chain C: C.56, P.57, I.60, T.97, C.101, Q.103, Q.106, C.107, I.122, E.126, I.453 7 PLIP interactions: 7 interactions with chain C, Salt bridges: C:E.126, C:E.126, C:E.126 Metal complexes: C:C.56, C:C.101, C:C.107, C:E.126 SF4.8: 7 residues within 4Å: Chain C: C.42, L.43, C.45, C.52, C.111, V.112, I.120 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.42, C:C.45, C:C.52, C:C.111

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)(Non-covalent)

FAD.3: 37 residues within 4Å: Chain A: V.100, I.160, G.161, A.162, G.163, P.164, A.165, Y.183, E.184, A.185, L.186, G.191, V.192, Y.195, G.196, I.197, R.201, V.225, L.226, V.227, G.246, T.247, G.248, L.272, N.303, T.304, D.307, R.333, Q.405, F.411, G.443, D.444, E.449, A.450, T.451, V.452, A.455 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:V.192, A:I.197, A:L.272, A:N.303, A:T.304 Hydrogen bonds: A:V.100, A:A.162, A:G.163, A:G.163, A:A.165, A:A.185, A:L.186, A:V.192, A:R.201, A:R.201, A:V.227, A:V.227, A:N.303, A:D.444, A:A.450, A:A.450, A:V.452 Water bridges: A:G.166, A:G.191, A:A.249, A:A.249, A:D.444, A:A.445, A:A.445, A:I.453 FAD.4: 27 residues within 4Å: Chain B: F.39, E.49, R.50, I.51, P.52, L.53, T.54, V.68, A.69, Q.70, V.72, G.73, K.74, T.75, T.76, V.114, E.118, L.217, N.218, P.219, I.220, M.221, P.247, L.263, A.264, E.270 Ligands: MG.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.39, B:P.52, B:P.52 Hydrogen bonds: B:T.54, B:T.54, B:V.68, B:Q.70, B:K.74, B:T.75, B:T.75, B:T.76, B:M.221, B:M.221, B:L.263, B:E.270, B:E.270 Water bridges: B:L.263, B:E.270 FAD.9: 37 residues within 4Å: Chain C: V.100, I.160, G.161, A.162, G.163, P.164, A.165, Y.183, E.184, A.185, L.186, G.191, V.192, Y.195, G.196, I.197, R.201, V.225, L.226, V.227, G.246, T.247, G.248, L.272, N.303, T.304, D.307, R.333, Q.405, F.411, G.443, D.444, E.449, A.450, T.451, V.452, A.455 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:V.192, C:I.197, C:L.272, C:N.303, C:T.304 Hydrogen bonds: C:V.100, C:A.162, C:G.163, C:G.163, C:A.165, C:A.185, C:L.186, C:V.192, C:R.201, C:R.201, C:V.227, C:V.227, C:N.303, C:D.444, C:A.450, C:A.450, C:V.452 Water bridges: C:G.166, C:G.191, C:A.249, C:D.444, C:A.445, C:A.445, C:T.451, C:I.453 FAD.10: 27 residues within 4Å: Chain D: F.39, E.49, R.50, I.51, P.52, L.53, T.54, V.68, A.69, Q.70, V.72, G.73, K.74, T.75, T.76, V.114, E.118, L.217, N.218, P.219, I.220, M.221, P.247, L.263, A.264, E.270 Ligands: MG.12 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:F.39, D:P.52, D:P.52 Hydrogen bonds: D:T.54, D:V.68, D:Q.70, D:K.74, D:T.75, D:T.76, D:M.221, D:M.221, D:L.263, D:E.270 Water bridges: D:L.263, D:E.270, D:E.270

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

FES.5: 11 residues within 4Å: Chain B: M.221, V.222, D.223, G.224, G.226, M.227, C.228, G.229, C.231, F.241, C.243 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:D.223, B:C.228, B:C.231, B:C.243 FES.11: 11 residues within 4Å: Chain D: M.221, V.222, D.223, G.224, G.226, M.227, C.228, G.229, C.231, F.241, C.243 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:D.223, D:C.228, D:C.231, D:C.243

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain B: E.49 Ligands: FAD.4 5 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:E.49, FAD.4, H2O.23, H2O.24, H2O.29 MG.12: 2 residues within 4Å: Chain D: E.49 Ligands: FAD.10 5 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: D:E.49, FAD.10, H2O.63, H2O.64, H2O.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lubner, C.E. et al., Mechanistic insights into energy conservation by flavin-based electron bifurcation. Nat. Chem. Biol. (2017)

Release Date

2017-04-12

Peptides

NADH-dependent Ferredoxin:NADP Oxidoreductase subunit alpha: AC
NADH-dependent Ferredoxin:NADP Oxidoreductase subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
L

B
S

D
S

NADH-dependent Ferredoxin:NADP Oxidoreductase subunit alpha

NADH-dependent Ferredoxin:NADP Oxidoreductase subunit beta

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