SMTL ID : 2eix.1

The Structure of Physarum polycephalum cytochrome b5 reductase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

4 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 1 residues within 4Å: Chain A: N.32 Ligand excluded by PLIP IOD.2: 1 residues within 4Å: Chain A: K.143 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: S.49, R.61, P.62 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain B: S.49, R.61, P.62 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: P.220, M.221 Ligands: NA.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.221 NA.8: 3 residues within 4Å: Chain B: P.220, M.221 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.221

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

FAD.5: 27 residues within 4Å: Chain A: H.47, R.61, P.62, Y.63, T.64, I.78, I.79, K.80, Y.82, K.84, G.85, Q.86, M.87, S.88, T.126, T.129, P.130, F.243 Chain B: F.195, V.196, M.221, M.222, K.224, A.225, M.226, H.229 Ligands: GOL.10 28 PLIP interactions: 22 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:P.62, A:F.243 Hydrogen bonds: A:P.62, A:Y.63, A:T.64, A:I.78, A:K.80, A:K.84, A:Q.86, A:M.87, A:S.88, A:T.126, A:T.129, B:V.196, B:K.224 Water bridges: A:R.61, A:R.61, A:I.78, A:E.83, A:E.83, A:E.83, B:V.196, B:K.224 Salt bridges: A:R.61, A:R.61 pi-Stacking: A:Y.63, B:F.195, B:F.195 FAD.9: 27 residues within 4Å: Chain A: F.195, V.196, M.221, M.222, K.224, A.225, M.226, H.229 Chain B: H.47, R.61, P.62, Y.63, T.64, I.78, I.79, K.80, Y.82, K.84, G.85, Q.86, M.87, S.88, T.126, T.129, P.130, F.243 Ligands: GOL.6 25 PLIP interactions: 19 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:P.62 Hydrogen bonds: B:P.62, B:Y.63, B:T.64, B:I.78, B:K.80, B:K.84, B:Q.86, B:M.87, B:S.88, B:T.126, B:T.129, A:V.196, A:K.224 Water bridges: B:R.61, B:R.61, B:R.61, B:I.78, A:V.196, A:K.224 Salt bridges: B:R.61, B:R.61 pi-Stacking: B:Y.63, A:F.195, A:F.195

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: M.221, K.224 Chain B: Y.82, G.218, P.219, P.220 Ligands: FAD.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.224, B:G.218 GOL.10: 7 residues within 4Å: Chain A: Y.82, G.218, P.219, P.220 Chain B: M.221, K.224 Ligands: FAD.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.218, B:K.224 Water bridges: B:K.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S. et al., Structure of Physarum polycephalum cytochrome b5 reductase at 1.56 A resolution. Acta Crystallogr.,Sect.F (2007)

Release Date

2007-04-17

Peptides

NADH-cytochrome b5 reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NADH-cytochrome b5 reductase