SMTL ID : 5jca.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 15 residues within 4Å: Chain A: C.56, P.57, I.60, I.62, N.91, T.97, G.98, C.101, Q.103, Q.106, C.107, I.122, G.123, 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: 14 residues within 4Å: Chain A: C.42, L.43, Q.44, C.45, A.50, P.51, C.52, I.62, P.63, C.111, V.112, V.113, I.120, I.122 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.42, A:C.45, A:C.52, A:C.111

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

FAD.3: 44 residues within 4Å: Chain A: V.100, C.101, P.102, I.160, G.161, A.162, G.163, P.164, A.165, G.166, 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, A.249, L.272, N.303, T.304, D.307, R.333, Q.405, F.411, G.443, D.444, A.445, E.449, A.450, T.451, V.452, A.455 Chain B: M.227 Ligands: NDP.4 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:Y.183, A:A.185, A:L.186, A:V.192, A:R.201, A:R.201, A:V.227, A:V.227, A:A.249, A:N.303, A:D.444, A:A.450, A:A.450, A:T.451, A:V.452 Water bridges: A:G.191, A:G.248, A:D.444, A:A.445, A:I.453 FAD.6: 28 residues within 4Å: Chain B: F.39, M.41, 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.8 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:V.68, B:Q.70, B:K.74, B:T.75, B:T.75, B:T.76, B:T.76, B:M.221, B:M.221, B:L.263, B:E.270 Water bridges: B:N.218, B:L.263, B:E.270

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Covalent)

NDP.4: 28 residues within 4Å: Chain A: R.253, Y.255, W.257, I.299, G.300, G.301, G.302, N.303, T.304, A.305, Y.323, R.324, R.325, T.331, A.332, R.333, T.352, P.353, R.382, P.385, A.402, I.403, G.404, Q.405, E.449, A.450, T.451 Ligands: FAD.3 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:N.303 Hydrogen bonds: A:R.253, A:G.302, A:G.302, A:T.304, A:T.304, A:A.305, A:Y.323, A:R.324, A:R.324, A:T.331, A:G.404, A:Q.405, A:Q.405, A:E.449, A:E.449 Water bridges: A:R.253, A:Y.255, A:Y.323, A:T.352, A:R.382, A:R.382, A:R.382, A:R.382, A:Q.405, A:Q.405 Salt bridges: A:R.253, A:R.324, A:R.325, A:R.382 pi-Cation interactions: A:R.324, A:R.324

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: L.236, R.237, Y.240, D.241, A.242, I.243, I.436, P.437, G.438, V.439 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.237, A:R.237, A:R.237 Water bridges: A:R.237, A:R.237, A:Y.240

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

FES.7: 12 residues within 4Å: Chain B: M.221, V.222, D.223, G.224, G.226, M.227, C.228, G.229, A.230, 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain B: E.49, T.75, E.270 Ligands: FAD.6 5 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:E.49, FAD.6, H2O.24, H2O.25, H2O.29

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 (NfnI) subunit alpha: A
NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
S

NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit alpha

NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit beta

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