MolNFT v1 · #146875 · protein
Lactate monooxygenase from mycobacterium smegmatis - C203A mutant
6DVH · Lactate 2-monooxygenase: “Lactate monooxygenase from mycobacterium smegmatis - C203A mutant”. X-ray diffraction, 2 ligands (FMN, SO4), 20 pockets (best druggability 0.83). MolNFT v1 #146875 on GenesisL1: 3D structure, binding sites…
- PDB
- 6DVH
- Type
- protein
- Length
- 2,363 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate 2-monooxygenase
- EC
- 1.13.12.4
- UniProt
- P21795
- Ligands
- FMN, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Lactate 2-monooxygenase (EC 1.13.12.4) | protein | 394 | 51% helix, 12% strand | P21795 |
| F | Lactate 2-monooxygenase (EC 1.13.12.4) | protein | 393 | 51% helix, 12% strand | P21795 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.83 | 0.95 | 39 | FMN, SO4 |
| 2 | 185 | 0.82 | 0.97 | 36 | FMN, SO4 |
| 3 | 168 | 0.81 | 0.97 | 35 | FMN, SO4 |
| 4 | 179 | 0.81 | 0.96 | 33 | FMN, SO4 |
| 5 | 241 | 0.80 | 0.93 | 44 | FMN, SO4 |
Interfaces
5 interfaces between chains.
- B–D · 718 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 712 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 239 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 230 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DVH · Lactate Monooxygenase from Mycobacterium smegmatis - C203A mutant · the same entry in another collection · chain F against F, TM-score 1.00
- P21795 · AlphaFold monomer V2.0 prediction for lactate 2-monooxygenase (P21795) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P21795
- Elsewhere: RCSB PDB 6DVH · PDBe 6DVH · UniProt P21795
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