Research workbench
Aerococcus viridans L-lactate oxidase Y215F mutant
Analyse Aerococcus viridans L-lactate oxidase Y215F mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EBU
- Type
- protein
- Length
- 2,905 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate oxidase
- EC
- 1.1.3.-
- UniProt
- Q44467
- Ligands
- FMN, PYR
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G | L-lactate oxidase (EC 1.1.3.-) | protein | 367 | 44% helix, 13% strand | Q44467 |
| D | L-lactate oxidase (EC 1.1.3.-) | protein | 353 | 42% helix, 14% strand | Q44467 |
| H | L-lactate oxidase (EC 1.1.3.-) | protein | 350 | 44% helix, 15% strand | Q44467 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PYR · Pyruvic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.83 | 0.97 | 34 | FMN, PYR |
| 2 | 172 | 0.82 | 0.97 | 35 | FMN, PYR |
| 3 | 173 | 0.82 | 0.97 | 34 | FMN, PYR |
| 4 | 166 | 0.81 | 0.97 | 32 | FMN, PYR |
| 5 | 170 | 0.81 | 0.97 | 31 | FMN, PYR |
Interfaces
11 interfaces between chains.
- A–C · 1824 Ų buried · 32 hydrogen bonds · protein-protein
- E–G · 1823 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1817 Ų buried · 28 hydrogen bonds · protein-protein
- F–H · 1816 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 1812 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5EBU · Aerococcus viridans L-lactate oxidase Y215F mutant · the same entry in another collection · 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 Q44467
- Elsewhere: RCSB PDB 5EBU · PDBe 5EBU · UniProt Q44467
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