Research workbench
Crystal structure of L-amino acid oxidase from venom of naja atra
Analyse Crystal structure of L-amino acid oxidase from venom of naja atra in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z2G
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-amino acid oxidase
- Ligands
- FAD, NAG
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-amino acid oxidase | protein | 477 | 42% helix, 22% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.88 | 0.91 | 102 | FAD |
| 2 | 1054 | 0.88 | 0.89 | 122 | FAD |
| 3 | 336 | 0.77 | 0.88 | 41 | empty |
| 4 | 68 | 0.76 | 0.99 | 18 | empty |
| 5 | 574 | 0.75 | 0.82 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 2223 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5Z2G · Crystal Structure of L-amino acid oxidase from venom of Naja atra · 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
- Elsewhere: RCSB PDB 5Z2G · PDBe 5Z2G
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