SMTL ID : 6dvi.3 (2 other biounits)

Wild-type Lactate Monooxygenase from Mycobacterium smegmatis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

8 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 22 residues within 4Å: Chain A: V.46, A.97, P.98, I.99, G.100, V.101, S.129, Q.151, Y.153, T.179, K.267, H.291, G.292, R.294, D.321, S.322, G.323, I.324, R.325, G.344, R.345 Ligands: SO4.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.46, A:I.99, A:I.99, A:V.101 Hydrogen bonds: A:G.100, A:S.129, A:Q.151, A:K.267, A:K.267, A:G.292, A:S.322, A:G.323, A:I.324, A:R.345 Salt bridges: A:R.325, A:R.345 pi-Cation interactions: A:R.294 FMN.4: 22 residues within 4Å: Chain B: V.46, A.97, P.98, I.99, G.100, V.101, S.129, Q.151, Y.153, T.179, K.267, H.291, G.292, R.294, D.321, S.322, G.323, I.324, R.325, G.344, R.345 Ligands: SO4.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.46, B:I.99, B:I.99, B:V.101 Hydrogen bonds: B:G.100, B:S.129, B:Q.151, B:K.267, B:K.267, B:G.292, B:S.322, B:G.323, B:I.324, B:R.345 Salt bridges: B:R.325, B:R.345 pi-Cation interactions: B:R.294 FMN.7: 22 residues within 4Å: Chain C: V.46, A.97, P.98, I.99, G.100, V.101, S.129, Q.151, Y.153, T.179, K.267, H.291, G.292, R.294, D.321, S.322, G.323, I.324, R.325, G.344, R.345 Ligands: SO4.9 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:V.46, C:I.99, C:I.99, C:V.101 Hydrogen bonds: C:G.100, C:S.129, C:Q.151, C:K.267, C:K.267, C:G.292, C:S.322, C:G.323, C:I.324, C:R.345 Salt bridges: C:R.325, C:R.345 pi-Cation interactions: C:R.294 FMN.10: 22 residues within 4Å: Chain D: V.46, A.97, P.98, I.99, G.100, V.101, S.129, Q.151, Y.153, T.179, K.267, H.291, G.292, R.294, D.321, S.322, G.323, I.324, R.325, G.344, R.345 Ligands: SO4.12 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:V.46, D:I.99, D:I.99, D:V.101 Hydrogen bonds: D:G.100, D:S.129, D:Q.151, D:K.267, D:K.267, D:G.292, D:S.322, D:G.323, D:I.324, D:R.345 Salt bridges: D:R.325, D:R.345 pi-Cation interactions: D:R.294 FMN.13: 24 residues within 4Å: Chain E: Y.45, V.46, A.97, P.98, I.99, G.100, V.101, S.129, Q.151, Y.153, T.179, K.267, S.289, H.291, G.292, R.294, D.321, S.322, G.323, I.324, R.325, G.344, R.345 Ligands: SO4.14 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:Y.45, E:V.46, E:I.99, E:V.101 Hydrogen bonds: E:P.98, E:G.100, E:S.129, E:Q.151, E:Y.153, E:T.179, E:K.267, E:K.267, E:S.289, E:S.322, E:G.323, E:I.324, E:R.345 Salt bridges: E:R.325, E:R.345 pi-Cation interactions: E:R.294 FMN.16: 24 residues within 4Å: Chain F: Y.45, V.46, A.97, P.98, I.99, G.100, V.101, S.129, Q.151, Y.153, T.179, K.267, S.289, H.291, G.292, R.294, D.321, S.322, G.323, I.324, R.325, G.344, R.345 Ligands: SO4.17 20 PLIP interactions: 20 interactions with chain F Hydrophobic interactions: F:Y.45, F:V.46, F:I.99, F:V.101 Hydrogen bonds: F:P.98, F:G.100, F:S.129, F:Q.151, F:Y.153, F:T.179, F:K.267, F:K.267, F:S.289, F:S.322, F:G.323, F:I.324, F:R.345 Salt bridges: F:R.325, F:R.345 pi-Cation interactions: F:R.294 FMN.19: 24 residues within 4Å: Chain G: Y.45, V.46, A.97, P.98, I.99, G.100, V.101, S.129, Q.151, Y.153, T.179, K.267, S.289, H.291, G.292, R.294, D.321, S.322, G.323, I.324, R.325, G.344, R.345 Ligands: SO4.20 20 PLIP interactions: 20 interactions with chain G Hydrophobic interactions: G:Y.45, G:V.46, G:I.99, G:V.101 Hydrogen bonds: G:P.98, G:G.100, G:S.129, G:Q.151, G:Y.153, G:T.179, G:K.267, G:K.267, G:S.289, G:S.322, G:G.323, G:I.324, G:R.345 Salt bridges: G:R.325, G:R.345 pi-Cation interactions: G:R.294 FMN.22: 24 residues within 4Å: Chain H: Y.45, V.46, A.97, P.98, I.99, G.100, V.101, S.129, Q.151, Y.153, T.179, K.267, S.289, H.291, G.292, R.294, D.321, S.322, G.323, I.324, R.325, G.344, R.345 Ligands: SO4.23 20 PLIP interactions: 20 interactions with chain H Hydrophobic interactions: H:Y.45, H:V.46, H:I.99, H:V.101 Hydrogen bonds: H:P.98, H:G.100, H:S.129, H:Q.151, H:Y.153, H:T.179, H:K.267, H:K.267, H:S.289, H:S.322, H:G.323, H:I.324, H:R.345 Salt bridges: H:R.325, H:R.345 pi-Cation interactions: H:R.294

16 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: H.54, R.57, E.61 Chain C: K.64 Ligand excluded by PLIP SO4.3: 7 residues within 4Å: Chain A: Y.45, Y.153, F.185, R.188, H.291, R.294 Ligands: FMN.1 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain B: H.54, R.57, E.61 Chain D: K.64 Ligand excluded by PLIP SO4.6: 7 residues within 4Å: Chain B: Y.45, Y.153, F.185, R.188, H.291, R.294 Ligands: FMN.4 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: K.64 Chain C: H.54, R.57, E.61 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain C: Y.45, Y.153, F.185, R.188, H.291, R.294 Ligands: FMN.7 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: K.64 Chain D: H.54, R.57, E.61 Ligand excluded by PLIP SO4.12: 7 residues within 4Å: Chain D: Y.45, Y.153, F.185, R.188, H.291, R.294 Ligands: FMN.10 Ligand excluded by PLIP SO4.14: 7 residues within 4Å: Chain E: Y.45, Y.153, F.185, R.188, H.291, R.294 Ligands: FMN.13 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain E: K.64 Chain H: H.54, R.57 Ligand excluded by PLIP SO4.17: 7 residues within 4Å: Chain F: Y.45, Y.153, F.185, R.188, H.291, R.294 Ligands: FMN.16 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain F: K.64 Chain G: H.54, R.57 Ligand excluded by PLIP SO4.20: 7 residues within 4Å: Chain G: Y.45, Y.153, F.185, R.188, H.291, R.294 Ligands: FMN.19 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain E: H.54, R.57 Chain G: K.64 Ligand excluded by PLIP SO4.23: 7 residues within 4Å: Chain H: Y.45, Y.153, F.185, R.188, H.291, R.294 Ligands: FMN.22 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain F: H.54, R.57 Chain H: K.64 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kean, K.M. et al., Structure and role for active site lid of lactate monooxygenase from Mycobacterium smegmatis. Protein Sci. (2019)

Release Date

2018-10-03

Peptides

Lactate 2-monooxygenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
E

C
E

D
E

E
F

F
F

G
F

H
F

Lactate 2-monooxygenase

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