MolNFT v1 · #55018 · protein
The native structures of soluble human primary amine oxidase AOC3
2Y73 · Membrane primary amine oxidase: “The native structures of soluble human primary amine oxidase AOC3”. X-ray diffraction, 4 ligands (NAG, MAN, CA), 14 pockets (best druggability 0.87). MolNFT v1 #55018 on GenesisL1: 3D structure…
- PDB
- 2Y73
- Type
- protein
- Length
- 1,406 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane primary amine oxidase
- EC
- 1.4.3.21
- UniProt
- Q16853
- Ligands
- NAG, MAN, CA, CU
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane primary amine oxidase (EC 1.4.3.21) | protein | 705 | 16% helix, 42% strand | Q16853 |
| B | Membrane primary amine oxidase (EC 1.4.3.21) | protein | 701 | 15% helix, 42% strand | Q16853 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 4 copies · chains A, B
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- IMD · Imidazole · additive · 8 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.87 | 0.88 | 115 | empty |
| 2 | 450 | 0.79 | 0.87 | 46 | empty |
| 3 | 439 | 0.78 | 0.87 | 49 | empty |
| 4 | 508 | 0.74 | 0.82 | 46 | IMD |
| 5 | 503 | 0.74 | 0.82 | 41 | IMD |
Interfaces
1 interface between chains.
- A–B · 8479 Ų buried · 126 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide, 2 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 2Y73 · The native structures of soluble human primary amine oxidase AOC3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q16853 · AlphaFold monomer V2.0 prediction for membrane primary amine oxidase (Q16853) · 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 Q16853
- Elsewhere: RCSB PDB 2Y73 · PDBe 2Y73 · UniProt Q16853
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