SMTL ID : 1kbj.1

Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast Flavocytochrome b2: comparison with the Intact Wild-type Enzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 24 residues within 4Å: Chain A: Y.44, Y.45, S.96, A.97, T.98, A.99, S.129, Q.153, Y.155, T.181, K.250, S.272, H.274, G.275, R.277, D.310, G.311, G.312, R.314, L.332, G.333, R.334, L.337 Ligands: EDO.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.44, A:Y.45, A:R.334, A:L.337 Hydrogen bonds: A:S.96, A:A.97, A:A.99, A:S.129, A:Q.153, A:Y.155, A:T.181, A:K.250, A:K.250, A:S.272, A:G.311, A:G.312, A:G.333, A:R.334 Water bridges: A:H.55, A:H.274, A:V.313, A:R.314, A:R.334 Salt bridges: A:R.314, A:R.334 pi-Cation interactions: A:H.274 FMN.3: 24 residues within 4Å: Chain B: Y.44, Y.45, S.96, A.97, T.98, A.99, S.129, Q.153, Y.155, T.181, K.250, S.272, H.274, G.275, R.277, D.310, G.311, G.312, R.314, L.332, G.333, R.334, L.337 Ligands: EDO.4 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:Y.44, B:Y.45, B:R.334, B:L.337 Hydrogen bonds: B:S.96, B:A.97, B:A.99, B:S.129, B:Q.153, B:Y.155, B:T.181, B:K.250, B:K.250, B:S.272, B:G.275, B:G.311, B:G.312, B:G.333, B:R.334 Water bridges: B:H.55, B:H.274, B:V.313, B:R.334 Salt bridges: B:R.314, B:R.334 pi-Cation interactions: B:H.274 FMN.5: 24 residues within 4Å: Chain C: Y.44, Y.45, S.96, A.97, T.98, A.99, S.129, Q.153, Y.155, T.181, K.250, S.272, H.274, G.275, R.277, D.310, G.311, G.312, R.314, L.332, G.333, R.334, L.337 Ligands: EDO.6 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:Y.44, C:Y.45, C:R.334, C:L.337 Hydrogen bonds: C:S.96, C:A.97, C:A.99, C:S.129, C:Q.153, C:Y.155, C:T.181, C:K.250, C:K.250, C:S.272, C:G.311, C:G.312, C:G.333, C:R.334 Water bridges: C:H.55, C:H.274, C:V.313, C:R.314, C:R.334 Salt bridges: C:R.314, C:R.334 pi-Cation interactions: C:H.274 FMN.7: 24 residues within 4Å: Chain D: Y.44, Y.45, S.96, A.97, T.98, A.99, S.129, Q.153, Y.155, T.181, K.250, S.272, H.274, G.275, R.277, D.310, G.311, G.312, R.314, L.332, G.333, R.334, L.337 Ligands: EDO.8 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:Y.44, D:Y.45, D:R.334, D:L.337 Hydrogen bonds: D:S.96, D:A.97, D:A.99, D:S.129, D:Q.153, D:Y.155, D:T.181, D:K.250, D:K.250, D:S.272, D:G.275, D:G.311, D:G.312, D:G.333, D:R.334 Water bridges: D:H.55, D:H.274, D:V.313, D:R.334 Salt bridges: D:R.314, D:R.334 pi-Cation interactions: D:H.274

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: Y.44, L.131, Y.155, H.274, R.277 Ligands: FMN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.155, A:Y.155, A:R.277, A:R.277 EDO.4: 6 residues within 4Å: Chain B: Y.44, Y.155, R.190, H.274, R.277 Ligands: FMN.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.155, B:Y.155, B:R.190, B:R.190, B:R.277, B:R.277 EDO.6: 6 residues within 4Å: Chain C: Y.44, L.131, Y.155, H.274, R.277 Ligands: FMN.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.155, C:Y.155, C:R.277, C:R.277 EDO.8: 6 residues within 4Å: Chain D: Y.44, Y.155, R.190, H.274, R.277 Ligands: FMN.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.155, D:Y.155, D:R.190, D:R.190, D:R.277, D:R.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cunane, L.M. et al., Crystallographic study of the recombinant flavin-binding domain of Baker's yeast flavocytochrome b(2): comparison with the intact wild-type enzyme. Biochemistry (2002)

Release Date

2002-04-03

Peptides

CYTOCHROME B2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

CYTOCHROME B2