SMTL ID : 5ebu.1 (1 other biounit)

Aerococcus viridans L-lactate oxidase Y215F mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: Y.40, I.41, A.92, P.93, I.94, A.95, S.122, Q.144, Y.146, T.172, K.241, S.263, H.265, G.266, R.268, D.296, S.297, G.298, V.299, R.300, G.319, R.320 Ligands: PYR.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.40, A:I.41, A:I.94, A:I.94, A:R.320 Hydrogen bonds: A:P.93, A:A.95, A:Q.144, A:K.241, A:K.241, A:S.263, A:G.298, A:V.299, A:R.320 Water bridges: A:H.265, A:S.297, A:S.297, A:V.299, A:G.319 Salt bridges: A:R.300, A:R.320 FMN.3: 23 residues within 4Å: Chain B: Y.40, I.41, A.92, P.93, I.94, A.95, S.122, Q.144, Y.146, T.172, K.241, S.263, H.265, G.266, R.268, D.296, S.297, G.298, V.299, R.300, G.319, R.320 Ligands: PYR.4 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.40, B:I.94, B:I.94, B:R.320 Hydrogen bonds: B:P.93, B:A.95, B:S.122, B:Q.144, B:T.172, B:K.241, B:K.241, B:S.263, B:G.266, B:S.297, B:G.298, B:V.299, B:R.320 Water bridges: B:N.54, B:H.265, B:R.300, B:R.300, B:A.317, B:R.320 Salt bridges: B:R.300, B:R.320 FMN.5: 23 residues within 4Å: Chain C: Y.40, I.41, A.92, P.93, I.94, A.95, S.122, Q.144, Y.146, T.172, K.241, S.263, H.265, G.266, R.268, D.296, S.297, G.298, V.299, R.300, G.319, R.320 Ligands: PYR.6 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:Y.40, C:I.94, C:I.94, C:R.320 Hydrogen bonds: C:P.93, C:A.95, C:S.122, C:Q.144, C:Q.144, C:K.241, C:K.241, C:S.263, C:H.265, C:G.266, C:S.297, C:G.298, C:V.299, C:R.320 Water bridges: C:A.317 Salt bridges: C:R.300, C:R.320 FMN.7: 23 residues within 4Å: Chain D: Y.40, I.41, A.92, P.93, I.94, A.95, S.122, Q.144, Y.146, T.172, K.241, S.263, H.265, G.266, R.268, D.296, S.297, G.298, V.299, R.300, G.319, R.320 Ligands: PYR.8 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:Y.40, D:I.94, D:I.94, D:R.320 Hydrogen bonds: D:P.93, D:A.95, D:S.122, D:Q.144, D:K.241, D:K.241, D:S.263, D:G.266, D:S.297, D:G.298, D:V.299, D:R.320 Water bridges: D:G.319, D:G.319 Salt bridges: D:R.300, D:R.320

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 10 residues within 4Å: Chain A: Y.40, Y.124, Y.146, R.181, Y.191, L.211, F.215, H.265, R.268 Ligands: FMN.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.124, A:L.211, A:F.215 Hydrogen bonds: A:Y.40 Salt bridges: A:R.181, A:H.265, A:R.268 PYR.4: 10 residues within 4Å: Chain B: Y.40, A.95, Y.124, Y.146, R.181, L.211, F.215, H.265, R.268 Ligands: FMN.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.95, B:Y.124, B:L.211, B:F.215 Hydrogen bonds: B:Y.40 Salt bridges: B:R.181, B:H.265, B:R.268 PYR.6: 11 residues within 4Å: Chain C: Y.40, A.95, Y.124, Y.146, R.181, Y.191, L.211, F.215, H.265, R.268 Ligands: FMN.5 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.95, C:Y.124, C:Y.146, C:L.211 Salt bridges: C:R.181, C:H.265, C:R.268 PYR.8: 6 residues within 4Å: Chain D: Y.40, Y.146, R.181, H.265, R.268 Ligands: FMN.7 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.40 Salt bridges: D:R.181, D:H.265, D:R.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stoisser, T. et al., Conformational flexibility related to enzyme activity: evidence for a dynamic active-site gatekeeper function of Tyr(215) in Aerococcus viridans lactate oxidase. Sci Rep (2016)

Release Date

2016-06-29

Peptides

L-lactate oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-lactate oxidase

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