Research workbench
The structure of L-amino acid oxidase from rhodococcus opacus in complex with O-aminobenzoate
Analyse The structure of L-amino acid oxidase from rhodococcus opacus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JB3
- Type
- protein
- Length
- 955 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-amino acid oxidase
- EC
- 1.4.3.2
- UniProt
- Q8VPD4
- Ligands
- FAD, BE2
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-amino acid oxidase (EC 1.4.3.2) | protein | 478 | 33% helix, 24% strand | Q8VPD4 |
| B | L-amino acid oxidase (EC 1.4.3.2) | protein | 477 | 32% helix, 24% strand | Q8VPD4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- BE2 · 2-aminobenzoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.82 | 0.86 | 109 | FAD, BE2 |
| 2 | 128 | 0.80 | 0.97 | 39 | empty |
| 3 | 676 | 0.79 | 0.84 | 100 | FAD, BE2 |
| 4 | 90 | 0.56 | 0.85 | 19 | empty |
| 5 | 79 | 0.55 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3750 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 2JB3 · The structure of L-amino acid oxidase from Rhodococcus opacus in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VPD4 · AlphaFold monomer V2.0 prediction for L-amino acid oxidase (Q8VPD4) · a predicted model of the same protein · chain B 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 Q8VPD4
- Elsewhere: RCSB PDB 2JB3 · PDBe 2JB3 · UniProt Q8VPD4
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