MolNFT v1 · #32795 · protein
The structure of a truncated, soluble version of semicarbazide- sensitive amine oxidase
2C10 · Membrane copper amine oxidase: “The structure of a truncated, soluble version of semicarbazide- sensitive amine oxidase”. X-ray diffraction, 7 ligands (NAG, BMA, FUC), 20 pockets (best druggability 0.87). MolNFT v1 #32795 on…
- PDB
- 2C10
- Type
- protein
- Length
- 2,826 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane copper amine oxidase
- EC
- 1.4.3.6
- UniProt
- Q16853
- Ligands
- NAG, BMA, FUC, MAN, CA, CU, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Membrane copper amine oxidase (EC 1.4.3.6) | protein | 705 | 16% helix, 42% strand | Q16853 |
| B, D | Membrane copper amine oxidase (EC 1.4.3.6) | protein | 708 | 15% helix, 42% strand | Q16853 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 6 copies
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.87 | 0.87 | 109 | empty |
| 2 | 1151 | 0.86 | 0.87 | 105 | empty |
| 3 | 425 | 0.78 | 0.87 | 48 | empty |
| 4 | 403 | 0.78 | 0.87 | 49 | empty |
| 5 | 405 | 0.78 | 0.87 | 48 | empty |
Interfaces
2 interfaces between chains.
- C–D · 8759 Ų buried · 123 hydrogen bonds · protein-protein
- A–B · 8743 Ų buried · 122 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 16 disulfide, 4 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 2C10 · The structure of a truncated, soluble version of semicarbazide- sensitive amine oxidase · the same entry in another collection · chain D against D, TM-score 1.00
- Q16853 · AlphaFold monomer V2.0 prediction for membrane primary amine oxidase (Q16853) · a predicted model of the same protein · chain C 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 2C10 · PDBe 2C10 · UniProt Q16853
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.