Research workbench
Crystal structure of L-lactate oxidase with pyruvate complex
Analyse Crystal structure of L-lactate oxidase with pyruvate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E77
- Type
- protein
- Length
- 1,441 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate oxidase
- EC
- 1.13.12.4
- UniProt
- Q44467
- Ligands
- FMN, PYR
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate oxidase (EC 1.13.12.4) | protein | 355 | 42% helix, 14% strand | Q44467 |
| B, D | Lactate oxidase (EC 1.13.12.4) | protein | 368 | 44% helix, 13% strand | Q44467 |
| C | Lactate oxidase (EC 1.13.12.4) | protein | 350 | 43% helix, 13% strand | Q44467 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- PYR · Pyruvic acid · ligand · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.82 | 0.97 | 32 | FMN, PYR |
| 2 | 152 | 0.81 | 0.98 | 32 | FMN, PYR |
| 3 | 512 | 0.74 | 0.82 | 61 | FMN, PYR |
| 4 | 453 | 0.74 | 0.83 | 55 | FMN |
| 5 | 91 | 0.61 | 0.89 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1814 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1806 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1796 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1785 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2E77 · Crystal structure of L-lactate oxidase with pyruvate complex · 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 2E77 · PDBe 2E77 · UniProt Q44467
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