SMTL ID : 1lco.1

X-RAY STRUCTURE OF TWO COMPLEXES OF THE Y143F FLAVOCYTOCHROME B2 MUTANT CRYSTALLIZED IN THE PRESENCE OF LACTATE OR PHENYL-LACTATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 27 residues within 4Å: Chain A: V.27, 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, A.67, V.70, I.71, I.75, Y.97, Q.139, F.143, L.199, L.230, A.231, K.296, F.325 Ligands: PPY.3 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:V.27, A:I.29, A:L.36, A:L.36, A:F.39, A:F.39, A:P.44, A:V.49, A:I.50, A:V.58, A:V.58, A:F.62, A:I.71, A:I.75, A:Y.97, A:L.199, A:L.199, A:L.230, A:L.230, A:F.325 Hydrogen bonds: A:A.67, A:Y.97, A:Q.139 Water bridges: A:R.289 Salt bridges: A:H.66, A:K.296 pi-Stacking: A:F.62 Metal complexes: A:H.43, A:H.66 HEM.6: 27 residues within 4Å: Chain C: V.27, 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, A.67, V.70, I.71, I.75, Y.97, Q.139, F.143, L.199, L.230, A.231, K.296, F.325 Ligands: PPY.8 29 PLIP interactions: 29 interactions with chain C, Hydrophobic interactions: C:V.27, C:I.29, C:L.36, C:L.36, C:F.39, C:F.39, C:P.44, C:V.49, C:I.50, C:V.58, C:V.58, C:F.62, C:I.71, C:I.75, C:Y.97, C:L.199, C:L.199, C:L.230, C:L.230, C:F.325 Hydrogen bonds: C:A.67, C:Y.97, C:Q.139 Water bridges: C:R.289 Salt bridges: C:H.66, C:K.296 pi-Stacking: C:F.62 Metal complexes: C:H.43, C:H.66

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 24 residues within 4Å: Chain A: F.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: PPY.3 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:F.143, A:Y.144, A:R.433, A:L.436 Hydrogen bonds: A:S.195, A:A.196, A:A.198, A:S.228, A:Q.252, A:Q.252, A:T.280, A:K.349, A:S.371, A:H.373, A:G.374, A:G.410, A:G.411, A:G.432, A:R.433 Water bridges: A:N.372, A:G.374, A:V.412, A:R.413, A:R.433 Salt bridges: A:R.413, A:R.433 FMN.4: 25 residues within 4Å: Chain B: F.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, V.412, R.413, L.431, G.432, R.433, L.436 Ligands: PPY.5 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.143, B:Y.144, B:R.433, B:L.436 Hydrogen bonds: B:S.195, B:A.196, B:A.198, B:S.228, B:Q.252, B:Y.254, B:T.280, B:K.349, B:S.371, B:G.410, B:G.411, B:G.432, B:R.433 Salt bridges: B:R.413, B:R.433 FMN.7: 24 residues within 4Å: Chain C: F.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: PPY.8 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:F.143, C:Y.144, C:R.433, C:L.436 Hydrogen bonds: C:S.195, C:A.196, C:A.198, C:S.228, C:Q.252, C:Q.252, C:T.280, C:K.349, C:S.371, C:H.373, C:G.374, C:G.410, C:G.411, C:G.432, C:R.433 Water bridges: C:N.372, C:G.374, C:V.412, C:R.413, C:R.433 Salt bridges: C:R.413, C:R.433 FMN.9: 25 residues within 4Å: Chain D: F.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, V.412, R.413, L.431, G.432, R.433, L.436 Ligands: PPY.10 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:F.143, D:Y.144, D:R.433, D:L.436 Hydrogen bonds: D:S.195, D:A.196, D:A.198, D:S.228, D:Q.252, D:Y.254, D:T.280, D:K.349, D:S.371, D:G.410, D:G.411, D:G.432, D:R.433 Salt bridges: D:R.413, D:R.433

4 x PPY: 3-PHENYLPYRUVIC ACID(Non-covalent)

PPY.3: 12 residues within 4Å: Chain A: G.45, F.143, A.198, L.199, L.230, Y.254, L.286, R.289, H.373, R.376 Ligands: HEM.1, FMN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.198, A:L.199, A:L.230 Hydrogen bonds: A:Y.254, A:R.289, A:R.376 Water bridges: A:H.373, A:R.376 Salt bridges: A:H.373, A:R.376 pi-Stacking: A:F.143 PPY.5: 7 residues within 4Å: Chain B: F.143, A.198, L.199, Y.254, H.373, R.376 Ligands: FMN.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.143, B:F.143, B:L.199, B:L.199 Hydrogen bonds: B:Y.254, B:Y.254, B:R.376 Salt bridges: B:H.373 PPY.8: 12 residues within 4Å: Chain C: G.45, F.143, A.198, L.199, L.230, Y.254, L.286, R.289, H.373, R.376 Ligands: HEM.6, FMN.7 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.198, C:L.199, C:L.230 Hydrogen bonds: C:Y.254, C:R.289, C:R.376 Water bridges: C:H.373, C:R.376 Salt bridges: C:H.373, C:R.376 pi-Stacking: C:F.143 PPY.10: 7 residues within 4Å: Chain D: F.143, A.198, L.199, Y.254, H.373, R.376 Ligands: FMN.9 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.143, D:F.143, D:L.199, D:L.199 Hydrogen bonds: D:Y.254, D:Y.254, D:R.376 Salt bridges: D:H.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tegoni, M. et al., X-ray structure of two complexes of the Y143F flavocytochrome b2 mutant crystallized in the presence of lactate or phenyl lactate. Biochemistry (1995)

Release Date

1995-09-15

Peptides

L-LACTATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-LACTATE DEHYDROGENASE

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