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The crystal structure of human soluble primary amine oxidase AOC3 in the off-copper conformation
Analyse The crystal structure of human soluble primary amine oxidase AOC3 in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y74
- Type
- protein
- Length
- 1,394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane primary amine oxidase
- EC
- 1.4.3.6
- UniProt
- Q16853
- Ligands
- NAG, MAN, CA, CU
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane primary amine oxidase (EC 1.4.3.6) | protein | 695 | 16% helix, 41% strand | Q16853 |
| B | Membrane primary amine oxidase (EC 1.4.3.6) | protein | 699 | 16% 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 · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.86 | 0.87 | 117 | empty |
| 2 | 470 | 0.80 | 0.88 | 48 | empty |
| 3 | 486 | 0.78 | 0.86 | 50 | empty |
| 4 | 457 | 0.72 | 0.82 | 39 | IMD |
| 5 | 388 | 0.71 | 0.82 | 37 | IMD |
Interfaces
1 interface between chains.
- A–B · 8337 Ų buried · 125 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 6 disulfide, 2 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 2Y74 · The crystal structure of human soluble primary amine oxidase AOC3 in the off-copper… · 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 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 Q16853
- Elsewhere: RCSB PDB 2Y74 · PDBe 2Y74 · UniProt Q16853
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