SMTL ID : 1kbi.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 2.30 Å

Oligo State

homo-tetramer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 25 residues within 4Å: Chain A: I.29, L.36, F.39, H.43, P.44, G.45, V.49, I.50, V.58, I.61, F.62, L.65, H.66, V.70, I.71, Y.74, I.75, Y.97, Q.139, Y.143, A.198, L.199, L.230, K.296, F.325 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:I.29, A:L.36, A:F.39, A:P.44, A:I.50, A:V.58, A:F.62, A:L.65, A:V.70, A:I.71, A:Y.74, A:I.75, A:I.75, A:L.230, A:F.325 Hydrogen bonds: A:Y.97, A:Q.139 Water bridges: A:R.289, A:K.296 Salt bridges: A:K.296 pi-Stacking: A:H.43, A:H.43, A:H.66, A:H.66 Metal complexes: A:H.43, A:H.66 HEM.11: 25 residues within 4Å: Chain C: I.29, L.36, F.39, H.43, P.44, G.45, V.49, I.50, V.58, I.61, F.62, L.65, H.66, V.70, I.71, Y.74, I.75, Y.97, Q.139, Y.143, A.198, L.199, L.230, K.296, F.325 26 PLIP interactions: 26 interactions with chain C, Hydrophobic interactions: C:I.29, C:L.36, C:F.39, C:P.44, C:I.50, C:V.58, C:F.62, C:L.65, C:V.70, C:I.71, C:Y.74, C:I.75, C:I.75, C:L.230, C:F.325 Hydrogen bonds: C:Q.139, C:Y.143 Water bridges: C:R.289, C:K.296 Salt bridges: C:K.296 pi-Stacking: C:H.43, C:H.43, C:H.66, C:H.66 Metal complexes: C:H.43, C:H.66

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 23 residues within 4Å: Chain A: Y.143, Y.144, S.195, A.196, T.197, A.198, S.228, Q.252, Y.254, T.280, K.349, S.371, H.373, G.374, R.376, D.409, G.410, G.411, R.413, L.431, G.432, R.433, L.436 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.143, A:Y.144, A:T.197, A:R.433, A:L.436 Hydrogen bonds: A:A.196, A:A.198, A:S.228, A:Q.252, A:Y.254, A:K.349, A:K.349, A:S.371, A:G.411, A:G.432, A:R.433 Water bridges: A:N.157, A:H.373, A:R.376, A:R.376, A:G.410, A:V.412, A:R.433 Salt bridges: A:R.413, A:R.433 FMN.8: 24 residues within 4Å: Chain B: Y.143, Y.144, S.195, A.196, T.197, A.198, S.228, Q.252, Y.254, T.280, K.349, S.371, H.373, G.374, R.376, D.409, G.410, G.411, R.413, L.431, G.432, R.433, L.436 Ligands: PYR.9 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.143, B:Y.144, B:R.433, B:L.436 Hydrogen bonds: B:A.196, B:A.198, B:Q.252, B:Y.254, B:K.349, B:K.349, B:S.371, B:G.411, B:G.432, B:R.433 Water bridges: B:N.157, B:H.373, B:G.410, B:G.410, B:R.433 Salt bridges: B:R.413, B:R.433 pi-Cation interactions: B:H.373 FMN.12: 23 residues within 4Å: Chain C: Y.143, Y.144, S.195, A.196, T.197, A.198, S.228, Q.252, Y.254, T.280, K.349, S.371, H.373, G.374, R.376, D.409, G.410, G.411, R.413, L.431, G.432, R.433, L.436 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:Y.143, C:Y.144, C:T.197, C:R.433, C:L.436 Hydrogen bonds: C:A.196, C:A.198, C:S.228, C:Q.252, C:T.280, C:K.349, C:K.349, C:S.371, C:G.411, C:G.432, C:R.433 Water bridges: C:Y.143, C:N.157, C:H.373, C:R.376, C:R.376, C:G.410, C:V.412, C:R.433 Salt bridges: C:R.413, C:R.433 FMN.18: 24 residues within 4Å: Chain D: Y.143, Y.144, S.195, A.196, T.197, A.198, S.228, Q.252, Y.254, T.280, K.349, S.371, H.373, G.374, R.376, D.409, G.410, G.411, R.413, L.431, G.432, R.433, L.436 Ligands: PYR.19 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:Y.143, D:Y.144, D:R.433, D:L.436 Hydrogen bonds: D:A.196, D:A.198, D:Q.252, D:T.280, D:K.349, D:K.349, D:S.371, D:G.411, D:G.432, D:R.433 Water bridges: D:N.157, D:H.373, D:G.410, D:G.410, D:R.433 Salt bridges: D:R.413, D:R.433 pi-Cation interactions: D:H.373

10 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: R.259, T.262, D.263, D.334, E.337, K.341 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.263, A:E.337, A:K.341 Hydrogen bonds: A:R.259 MPD.4: 5 residues within 4Å: Chain A: R.353, E.355, K.359 Chain D: K.169, D.476 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:E.355, D:K.169 Hydrogen bonds: A:R.353, A:K.359, D:K.169, D:K.169 Water bridges: A:R.353 MPD.5: 2 residues within 4Å: Chain A: D.182, G.185 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.182 Water bridges: A:H.187 MPD.6: 6 residues within 4Å: Chain A: T.354, E.355, E.390, I.394, R.398 Chain D: K.167 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:T.354 Hydrogen bonds: A:E.355, A:E.390, A:R.398, D:K.167 MPD.10: 7 residues within 4Å: Chain B: R.259, T.262, D.263, D.334, E.337, L.338, K.341 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.334, B:E.337, B:K.341 Hydrogen bonds: B:R.259 MPD.13: 6 residues within 4Å: Chain C: R.259, T.262, D.263, D.334, E.337, K.341 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:D.263, C:E.337, C:K.341 Hydrogen bonds: C:R.259 MPD.14: 5 residues within 4Å: Chain B: K.169, D.476 Chain C: R.353, E.355, K.359 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:K.169, C:E.355 Hydrogen bonds: B:K.169, B:K.169, B:D.476, C:R.353, C:K.359 Water bridges: C:R.353 MPD.15: 2 residues within 4Å: Chain C: D.182, G.185 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:D.182 Water bridges: C:H.187 MPD.16: 6 residues within 4Å: Chain B: K.167 Chain C: T.354, E.355, E.390, I.394, R.398 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.354 Hydrogen bonds: C:E.355, C:R.398, B:K.167 MPD.20: 7 residues within 4Å: Chain D: R.259, T.262, D.263, D.334, E.337, L.338, K.341 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:D.334, D:E.337, D:K.341 Hydrogen bonds: D:R.259

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 2 residues within 4Å: Chain B: T.487 Ligands: PO4.17 No protein-ligand interaction detected (PLIP) PO4.17: 2 residues within 4Å: Chain D: T.487 Ligands: PO4.7 No protein-ligand interaction detected (PLIP)

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.9: 6 residues within 4Å: Chain B: Y.143, L.230, Y.254, H.373, R.376 Ligands: FMN.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.230 Hydrogen bonds: B:Y.143, B:Y.254 Salt bridges: B:R.289, B:H.373, B:R.376 PYR.19: 6 residues within 4Å: Chain D: Y.143, L.230, Y.254, H.373, R.376 Ligands: FMN.18 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.230 Hydrogen bonds: D:Y.143, D:Y.143 Salt bridges: D:R.289, D:H.373, D:R.376

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

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