SMTL ID : 4h4x.1

Crystal Structure of Ferredoxin reductase, BphA4 E175A/T176R/Q177G mutant (oxidized form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 32 residues within 4Å: Chain A: G.14, G.16, L.17, A.18, V.38, G.39, D.40, E.41, R.48, P.49, S.52, K.53, V.80, T.81, A.82, A.108, T.109, G.110, A.111, L.129, R.130, I.156, E.159, L.243, G.272, D.273, E.289, T.290, W.291, A.294, Y.319, W.320 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:R.48, A:I.156, A:I.156, A:I.156 Hydrogen bonds: A:A.15, A:G.16, A:A.18, A:D.40, A:E.41, A:R.48, A:K.53, 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:R.48, A:G.110, A:R.130, A:N.240, A:V.274, A:S.292, A:A.294 Salt bridges: A:R.48, A:R.130 FAD.11: 32 residues within 4Å: Chain B: G.14, G.16, L.17, A.18, V.38, G.39, D.40, E.41, R.48, P.49, S.52, K.53, V.80, T.81, A.82, A.108, T.109, G.110, A.111, L.129, R.130, I.156, E.159, L.243, G.272, D.273, E.289, T.290, W.291, A.294, Y.319, W.320 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:R.48, B:I.156, B:I.156, B:I.156 Hydrogen bonds: B:A.15, B:G.16, B:A.18, B:D.40, B:E.41, B:E.41, B:R.48, B:K.53, 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:D.40, B:D.40, B:R.48, B:G.110, B:N.240, B:V.274, B:S.292, B:A.294 Salt bridges: B:R.48, B:R.130

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: P.113, T.128, L.129, I.156, V.233, G.234, I.235, G.236 Ligands: FMT.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.129, A:V.233, A:G.236, A:G.236 Water bridges: A:R.114, A:R.130 GOL.12: 9 residues within 4Å: Chain B: P.113, T.128, L.129, I.156, V.233, G.234, I.235, G.236 Ligands: FMT.18 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.129, B:V.233, B:G.236, B:G.236 Water bridges: B:R.114, B:R.130

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

FMT.3: 5 residues within 4Å: Chain A: A.115, L.116, V.126, T.128, V.233 Ligand excluded by PLIP FMT.4: 2 residues within 4Å: Chain A: V.217, R.225 Ligand excluded by PLIP FMT.5: 6 residues within 4Å: Chain A: T.109, N.240, D.241, A.242, L.243, A.244 Ligand excluded by PLIP FMT.6: 6 residues within 4Å: Chain A: D.54, F.55, H.58, G.59, D.60, K.63 Ligand excluded by PLIP FMT.7: 7 residues within 4Å: Chain A: A.122, T.123, M.124, S.213, V.214, D.215, G.216 Ligand excluded by PLIP FMT.8: 4 residues within 4Å: Chain A: G.154, V.155, I.156 Ligands: GOL.2 Ligand excluded by PLIP FMT.9: 4 residues within 4Å: Chain A: R.327, N.369, N.370, A.371 Ligand excluded by PLIP FMT.10: 7 residues within 4Å: Chain A: A.161, A.162, R.165, Y.196, H.197, Q.200, V.202 Ligand excluded by PLIP FMT.13: 5 residues within 4Å: Chain B: A.115, L.116, V.126, T.128, V.233 Ligand excluded by PLIP FMT.14: 2 residues within 4Å: Chain B: V.217, R.225 Ligand excluded by PLIP FMT.15: 6 residues within 4Å: Chain B: T.109, N.240, D.241, A.242, L.243, A.244 Ligand excluded by PLIP FMT.16: 6 residues within 4Å: Chain B: D.54, F.55, H.58, G.59, D.60, K.63 Ligand excluded by PLIP FMT.17: 7 residues within 4Å: Chain B: A.122, T.123, M.124, S.213, V.214, D.215, G.216 Ligand excluded by PLIP FMT.18: 4 residues within 4Å: Chain B: G.154, V.155, I.156 Ligands: GOL.12 Ligand excluded by PLIP FMT.19: 4 residues within 4Å: Chain B: R.327, N.369, N.370, A.371 Ligand excluded by PLIP FMT.20: 7 residues within 4Å: Chain B: A.161, A.162, R.165, Y.196, H.197, Q.200, V.202 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishizawa, A. et al., Random Mutagenesis with the Project Assessment for Complete Conversion of Co-Factor Specificity of a Ferredoxin Reductase BphA4. To be Published

Release Date

2013-10-09

Peptides

Biphenyl dioxygenase ferredoxin reductase subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Biphenyl dioxygenase ferredoxin reductase subunit

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