SMTL ID : 1ldc.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

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 26 residues within 4Å: Chain A: F.143, Y.144, H.154, 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: PYR.3 23 PLIP interactions: 23 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.196, A:A.198, A:S.228, A:Q.252, A:Q.252, A:T.280, A:K.349, A:S.371, A:S.371, A:G.410, A:G.411, A:G.432, A:R.433 Water bridges: A:H.154, A:V.412 Salt bridges: A:R.413, A:R.433 FMN.4: 27 residues within 4Å: Chain B: F.143, Y.144, S.195, A.196, T.197, A.198, S.228, L.230, 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, G.430, L.431, G.432, R.433, L.436 Ligands: PYR.5 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.143, B:Y.144, B:R.433, B:L.436 Hydrogen bonds: B:A.196, B:A.198, B:S.228, B:Q.252, B:T.280, B:K.349, B:S.371, B:D.409, B:G.410, B:G.411, B:G.432, B:R.433 Salt bridges: B:R.413, B:R.433 FMN.6: 26 residues within 4Å: Chain C: F.143, Y.144, H.154, 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: PYR.8 23 PLIP interactions: 23 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.196, C:A.198, C:S.228, C:Q.252, C:Q.252, C:T.280, C:K.349, C:S.371, C:S.371, C:G.410, C:G.411, C:G.432, C:R.433 Water bridges: C:H.154, C:V.412 Salt bridges: C:R.413, C:R.433 FMN.9: 27 residues within 4Å: Chain D: F.143, Y.144, S.195, A.196, T.197, A.198, S.228, L.230, 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, G.430, L.431, G.432, R.433, L.436 Ligands: PYR.10 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:F.143, D:Y.144, D:R.433, D:L.436 Hydrogen bonds: D:A.196, D:A.198, D:S.228, D:Q.252, D:T.280, D:K.349, D:S.371, D:D.409, D:G.410, D:G.411, D:G.432, D:R.433 Salt bridges: D:R.413, D:R.433

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

HEM.2: 23 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, H.66, V.70, I.71, Y.74, I.75, Y.97, Q.139, F.143, L.199, L.230, K.296 Ligands: PYR.3 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:I.29, A:L.36, A:F.39, A:P.44, A:V.49, A:I.50, A:V.58, A:V.58, A:I.61, A:I.61, A:F.62, A:V.70, A:I.71, A:Y.74, A:I.75, A:I.75, A:Y.97, A:L.199, A:L.199, A:L.230 Hydrogen bonds: A:Q.139 Salt bridges: A:K.296 pi-Stacking: A:F.62, A:F.62 Metal complexes: A:H.43, A:H.66 HEM.7: 23 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, H.66, V.70, I.71, Y.74, I.75, Y.97, Q.139, F.143, L.199, L.230, K.296 Ligands: PYR.8 26 PLIP interactions: 26 interactions with chain C, Hydrophobic interactions: C:I.29, C:L.36, C:F.39, C:P.44, C:V.49, C:I.50, C:V.58, C:V.58, C:I.61, C:I.61, C:F.62, C:V.70, C:I.71, C:Y.74, C:I.75, C:I.75, C:Y.97, C:L.199, C:L.199, C:L.230 Hydrogen bonds: C:Q.139 Salt bridges: C:K.296 pi-Stacking: C:F.62, C:F.62 Metal complexes: C:H.43, C:H.66

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.3: 7 residues within 4Å: Chain A: F.143, Y.254, R.289, H.373, R.376 Ligands: FMN.1, HEM.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.373, A:R.376 Salt bridges: A:R.289, A:R.376 PYR.5: 8 residues within 4Å: Chain B: F.143, A.198, Y.254, L.286, R.289, H.373, R.376 Ligands: FMN.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.198, B:L.286 Hydrogen bonds: B:Y.254, B:H.373 Salt bridges: B:R.289, B:H.373, B:R.376 PYR.8: 7 residues within 4Å: Chain C: F.143, Y.254, R.289, H.373, R.376 Ligands: FMN.6, HEM.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.373, C:R.376 Salt bridges: C:R.289, C:R.376 PYR.10: 8 residues within 4Å: Chain D: F.143, A.198, Y.254, L.286, R.289, H.373, R.376 Ligands: FMN.9 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.198, D:L.286 Hydrogen bonds: D:Y.254, D:H.373 Salt bridges: D:R.289, D:H.373, D:R.376

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

1995-07-10

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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