MolNFT v1 · #34882 · protein
Crystal structure analysis of the L-lactate oxidase
2DU2: “Crystal structure analysis of the L-lactate oxidase”. X-ray diffraction, 1 ligand (FMN), 15 pockets (best druggability 0.82). MolNFT v1 #34882 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DU2
- Type
- protein
- Length
- 1,496 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
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lactate oxidase (EC 1.13.12.4) | protein | 374 | 41% helix, 14% strand | Q44467 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.82 | 0.97 | 32 | FMN |
| 2 | 154 | 0.81 | 0.97 | 33 | FMN |
| 3 | 151 | 0.81 | 0.97 | 31 | FMN |
| 4 | 148 | 0.80 | 0.97 | 32 | FMN |
| 5 | 113 | 0.64 | 0.88 | 24 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1834 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1819 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1807 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1801 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2DU2 · Crystal Structure Analysis of the L-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 2DU2 · PDBe 2DU2 · UniProt Q44467
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