MolNFT v1 · #22703 · protein
L-amino acid oxidase from agkistrodon halys in complex with suicide substrate L-vinylglycine
1TDK: “L-amino acid oxidase from agkistrodon halys in complex with suicide substrate L-vinylglycine”. X-ray diffraction, 3 ligands (LVG, FAD, NAG), 3 pockets (best druggability 0.86). MolNFT v1 #22703 on GenesisL1: 3D structure, binding…
- PDB
- 1TDK
- Type
- protein
- Length
- 484 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-amino acid oxidase
- EC
- 1.4.3.2
- UniProt
- Q90W54
- Ligands
- LVG, FAD, NAG
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-amino acid oxidase (EC 1.4.3.2) | protein | 484 | 42% helix, 22% strand | Q90W54 |
Ligands and binding sites
- LVG · L-vinylglycine · ligand · 2 copies · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.86 | 0.87 | 125 | FAD, LVG |
| 2 | 55 | 0.72 | 0.98 | 15 | empty |
| 3 | 167 | 0.55 | 0.80 | 29 | empty |
Modifications
Observed in the structure: 2 disulfide, 2 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 1TDK · L-amino acid oxidase from Agkistrodon halys in complex with suicide substrate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q90W54 · AlphaFold monomer V2.0 prediction for L-amino-acid oxidase (Q90W54) · a predicted model of the same protein · 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 Q90W54
- Elsewhere: RCSB PDB 1TDK · PDBe 1TDK · UniProt Q90W54
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