SMTL ID : 2yvf.1

Crystal structure of ferredoxin reductase BPHA4 (hydroquinone)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 34 residues within 4Å: Chain A: G.14, A.15, G.16, L.17, A.18, V.38, G.39, D.40, E.41, R.48, P.49, S.52, V.80, T.81, A.82, A.108, T.109, G.110, A.111, L.129, R.130, I.156, E.159, N.240, G.272, D.273, E.289, T.290, W.291, A.294, Y.319, W.320, S.321 Ligands: NAD.2 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:R.48, A:L.129, A:I.156, A:I.156 Hydrogen bonds: A:G.14, A:A.15, A:G.16, A:A.18, A:D.40, A:E.41, A:E.41, A:R.48, A:A.82, A:A.82, A:A.111, A:D.273, A:E.289, A:W.291, A:W.320 Water bridges: A:L.17, A:L.17, A:S.19, A:D.40, A:D.40, A:R.48, A:R.48, A:D.273, A:V.274, A:S.292, A:D.322 Salt bridges: A:R.48, A:R.130 pi-Stacking: A:W.320 FAD.8: 34 residues within 4Å: Chain B: G.14, A.15, G.16, L.17, A.18, V.38, G.39, D.40, E.41, R.48, P.49, S.52, V.80, T.81, A.82, A.108, T.109, G.110, A.111, L.129, R.130, I.156, E.159, N.240, G.272, D.273, E.289, T.290, W.291, A.294, Y.319, W.320, S.321 Ligands: NAD.9 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:R.48, B:L.129, B:I.156, B:I.156 Hydrogen bonds: B:G.14, B:A.15, B:G.16, B:A.18, B:D.40, B:E.41, B:R.48, B:A.82, B:A.82, B:A.111, B:D.273, B:E.289, B:W.291, B:W.320 Water bridges: B:L.17, B:L.17, B:S.19, B:R.48, B:R.48, B:V.274, B:S.292, B:D.322 Salt bridges: B:R.48, B:R.130 pi-Stacking: B:W.320

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 25 residues within 4Å: Chain A: R.114, L.116, R.130, V.151, G.152, G.153, G.154, V.155, I.156, V.174, E.175, T.176, Q.177, S.182, R.183, A.184, G.234, I.235, G.236, V.237, D.273, E.289, T.290, Y.319 Ligands: FAD.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:V.155, A:Y.319 Hydrogen bonds: A:R.114, A:R.130, A:R.130, A:G.153, A:G.153, A:V.155, A:I.156, A:T.176, A:T.176, A:S.182, A:R.183, A:R.183, A:G.234, A:G.236, A:D.273, A:E.289, A:E.289 Water bridges: A:G.154, A:G.157, A:S.182, A:S.182, A:V.210, A:V.237 Salt bridges: A:R.183 NAD.9: 25 residues within 4Å: Chain B: R.114, L.116, R.130, V.151, G.152, G.153, G.154, V.155, I.156, V.174, E.175, T.176, Q.177, S.182, R.183, A.184, G.234, I.235, G.236, V.237, D.273, E.289, T.290, Y.319 Ligands: FAD.8 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:V.155, B:Y.319 Hydrogen bonds: B:R.114, B:R.130, B:R.130, B:G.153, B:G.153, B:V.155, B:I.156, B:T.176, B:T.176, B:S.182, B:R.183, B:R.183, B:G.234, B:G.236, B:D.273, B:E.289 Water bridges: B:G.154, B:G.157, B:S.182, B:S.182, B:V.210, B:V.237 Salt bridges: B:R.183

10 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: D.54, F.55, H.58, G.59, D.60, K.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.58, A:D.60 FMT.4: 7 residues within 4Å: Chain A: A.122, T.123, M.124, S.213, V.214, D.215, G.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.123, A:M.124, A:S.213, A:G.216 FMT.5: 4 residues within 4Å: Chain A: R.327, N.369, N.370, A.371 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.327, A:A.371 FMT.6: 2 residues within 4Å: Chain A: W.320, D.322 No protein-ligand interaction detected (PLIP) FMT.7: 4 residues within 4Å: Chain A: A.115, L.116, V.126, V.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.116 FMT.10: 6 residues within 4Å: Chain B: D.54, F.55, H.58, G.59, D.60, K.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.60 FMT.11: 7 residues within 4Å: Chain B: A.122, T.123, M.124, S.213, V.214, D.215, G.216 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.123, B:T.123, B:M.124, B:S.213, B:G.216 FMT.12: 4 residues within 4Å: Chain B: R.327, N.369, N.370, A.371 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.327, B:A.371 FMT.13: 2 residues within 4Å: Chain B: W.320, D.322 No protein-ligand interaction detected (PLIP) FMT.14: 4 residues within 4Å: Chain B: A.115, L.116, V.126, V.233 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Senda, M. et al., Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin. J.Mol.Biol. (2007)

Release Date

2007-10-16

Peptides

Ferredoxin reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ferredoxin reductase

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