SMTL ID : 4rje.1

Aerococcus viridans L-lactate oxidase mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

4 x FNR: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL(Non-covalent)

FNR.1: 23 residues within 4Å: Chain A: Y.40, I.41, A.92, P.93, I.94, G.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 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:Y.40, A:I.94, A:I.94, A:R.320 Hydrogen bonds: A:P.93, A:G.95, A:S.122, A:Q.144, A:K.241, A:K.241, A:K.241, A:S.263, A:H.265, A:G.298, A:V.299, A:R.320 Water bridges: A:Y.40, A:N.54, A:G.95, A:S.297, A:S.297, A:G.319, A:G.319, A:R.320 Salt bridges: A:R.300, A:R.320 pi-Cation interactions: A:R.268 FNR.4: 22 residues within 4Å: Chain B: I.41, A.92, P.93, I.94, G.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.5 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.94, B:I.94, B:R.320 Hydrogen bonds: B:P.93, B:G.95, B:S.122, B:Q.144, B:K.241, B:K.241, B:K.241, B:S.263, B:H.265, B:G.266, B:S.297, B:G.298, B:V.299, B:R.320 Water bridges: B:N.54, B:G.319, B:R.320 Salt bridges: B:R.300, B:R.320 pi-Cation interactions: B:R.268 FNR.7: 23 residues within 4Å: Chain C: Y.40, I.41, A.92, P.93, I.94, G.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 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:Y.40, C:I.94, C:I.94, C:R.320 Hydrogen bonds: C:P.93, C:G.95, C:S.122, C:Q.144, C:K.241, C:K.241, C:K.241, C:S.263, C:H.265, C:S.297, C:G.298, C:V.299, C:R.320 Water bridges: C:Y.40, C:G.95, C:G.266, C:G.319, C:G.319, C:R.320 Salt bridges: C:R.300, C:R.320 FNR.10: 24 residues within 4Å: Chain D: Y.40, I.41, A.92, P.93, I.94, G.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, L.323 Ligands: PYR.11 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:Y.40, D:I.94, D:I.94, D:R.320, D:L.323 Hydrogen bonds: D:P.93, D:G.95, D:S.122, D:Q.144, D:K.241, D:K.241, D:K.241, D:S.263, D:H.265, D:G.266, D:G.298, D:V.299, D:R.320 Water bridges: D:Y.40, D:G.266, D:S.297, D:R.300, D:G.319, D:R.320 Salt bridges: D:R.300, D:R.320 pi-Cation interactions: D:R.268

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 9 residues within 4Å: Chain A: Y.40, Y.124, Y.146, R.181, L.211, Y.215, H.265, R.268 Ligands: FNR.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.124, A:L.211 Hydrogen bonds: A:Y.40, A:Y.215 Salt bridges: A:R.181, A:H.265, A:R.268 PYR.5: 10 residues within 4Å: Chain B: Y.40, Y.124, Y.146, R.181, Y.191, L.211, Y.215, H.265, R.268 Ligands: FNR.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.124, B:L.211 Hydrogen bonds: B:Y.40, B:Y.191, B:Y.215 Salt bridges: B:R.181, B:H.265, B:R.268 PYR.8: 8 residues within 4Å: Chain C: Y.40, Y.124, Y.146, R.181, L.211, H.265, R.268 Ligands: FNR.7 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.124, C:L.211 Hydrogen bonds: C:Y.40 Salt bridges: C:R.181, C:H.265, C:R.268 PYR.11: 9 residues within 4Å: Chain D: Y.40, Y.124, Y.146, R.181, L.211, Y.215, H.265, R.268 Ligands: FNR.10 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.124, D:L.211 Hydrogen bonds: D:Y.40, D:Y.215 Salt bridges: D:R.181, D:H.265, D:R.268

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

EDO.3: 3 residues within 4Å: Chain A: E.26, K.51, R.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.26, A:K.51, A:R.300 Water bridges: A:K.51 EDO.6: 3 residues within 4Å: Chain B: E.26, K.51, R.300 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.26, B:K.51, B:R.300 Water bridges: B:K.51, B:D.55, B:R.300 EDO.9: 3 residues within 4Å: Chain C: E.26, K.51, R.300 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.26, C:K.51, C:R.300 Water bridges: C:K.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stoisser, T. et al., The Ala95-to-Gly substitution in Aerococcus viridans l-lactate oxidase revisited - structural consequences at the catalytic site and effect on reactivity with O2 and other electron acceptors. Febs J. (2015)

Release Date

2014-12-03

Peptides

Lactate oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Lactate oxidase