Research workbench
Wild-type lactate monooxygenase from mycobacterium smegmatis
Analyse Wild-type lactate monooxygenase from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DVI
- Type
- protein
- Length
- 2,306 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 0.81
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Lactate 2-monooxygenase (EC 1.13.12.4) | protein | 394 | 51% helix, 12% strand | P21795 |
| D | Lactate 2-monooxygenase (EC 1.13.12.4) | protein | 338 | 41% helix, 14% strand | P21795 |
| E, F | Lactate 2-monooxygenase (EC 1.13.12.4) | protein | 393 | 45% 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 · 19 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.81 | 0.97 | 36 | FMN, SO4 |
| 2 | 160 | 0.81 | 0.96 | 35 | FMN, SO4 |
| 3 | 245 | 0.80 | 0.93 | 41 | FMN, SO4 |
| 4 | 158 | 0.80 | 0.96 | 34 | FMN, SO4 |
| 5 | 249 | 0.79 | 0.92 | 43 | FMN, SO4 |
Interfaces
4 interfaces between chains.
- A–C · 703 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 637 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 316 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 247 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 6DVI · PDBe 6DVI · UniProt P21795
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