MolNFT v1 · #40891 · protein
The crystal structure of lactate oxidase
2J6X: “The crystal structure of lactate oxidase”. X-ray diffraction, 2 ligands (FMN, ZN), 20 pockets (best druggability 0.82). MolNFT v1 #40891 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2J6X
- Type
- protein
- Length
- 2,897 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate oxidase
- EC
- 1.1.3.2
- UniProt
- Q44467
- Ligands
- FMN, ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate oxidase (EC 1.1.3.2) | protein | 370 | 42% helix, 13% strand | Q44467 |
| B, E, G | Lactate oxidase (EC 1.1.3.2) | protein | 367 | 43% helix, 13% strand | Q44467 |
| C | Lactate oxidase (EC 1.1.3.2) | protein | 368 | 44% helix, 14% strand | Q44467 |
| D | Lactate oxidase (EC 1.1.3.2) | protein | 353 | 42% helix, 14% strand | Q44467 |
| F | Lactate oxidase (EC 1.1.3.2) | protein | 357 | 43% helix, 14% strand | Q44467 |
| H | Lactate oxidase (EC 1.1.3.2) | protein | 348 | 44% helix, 14% strand | Q44467 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.82 | 0.96 | 32 | FMN |
| 2 | 159 | 0.82 | 0.98 | 33 | FMN |
| 3 | 160 | 0.81 | 0.97 | 33 | FMN |
| 4 | 280 | 0.80 | 0.92 | 43 | FMN |
| 5 | 258 | 0.78 | 0.91 | 46 | FMN |
Interfaces
13 interfaces between chains.
- G–H · 1830 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1821 Ų buried · 31 hydrogen bonds · protein-protein
- E–G · 1817 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1813 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1807 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 2J6X · The crystal structure of lactate oxidase · 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 2J6X · PDBe 2J6X · UniProt Q44467
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