Research workbench
Aerococcus viridans L-lactate oxidase Y191F mutant
Analyse Aerococcus viridans L-lactate oxidase Y191F mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YL2
- Type
- protein
- Length
- 1,466 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate oxidase
- UniProt
- Q44467
- Ligands
- FMN, PYR
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Lactate oxidase | protein | 367 | 44% helix, 12% strand | Q44467 |
| D | Lactate oxidase | protein | 365 | 44% helix, 13% strand | Q44467 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.82 | 0.98 | 30 | FMN, PYR |
| 2 | 143 | 0.80 | 0.97 | 30 | FMN, PYR |
| 3 | 211 | 0.78 | 0.92 | 40 | FMN, PYR |
| 4 | 271 | 0.77 | 0.90 | 54 | FMN, PYR |
| 5 | 87 | 0.62 | 0.90 | 24 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1811 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1794 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1790 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1789 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4YL2 · Aerococcus viridans L-lactate oxidase Y191F 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 4YL2 · PDBe 4YL2 · UniProt Q44467
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