MolNFT v1 · #60676 · protein
Dimeric crystal structure of a pheromone binding protein from apis mellifera in complex with 9-keto-2(E)-decenoic acid at pH 7.0
3CYZ · Pheromone-binding protein ASP1: “Dimeric crystal structure of a pheromone binding protein from apis mellifera in complex with…”. X-ray diffraction, 3 ligands (9OD, MG, CL), 3 pockets (best druggability 0.85). MolNFT v1 #60676 on…
- PDB
- 3CYZ
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pheromone-binding protein ASP1
- UniProt
- Q9U9J6
- Ligands
- 9OD, MG, CL
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pheromone-binding protein ASP1 | protein | 116 | 59% helix, 9% strand | Q9U9J6 |
| B | Pheromone-binding protein ASP1 | protein | 115 | 60% helix, 9% strand | Q9U9J6 |
Ligands and binding sites
- 9OD · (2Z)-9-oxodec-2-enoic acid · ligand · 3 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.85 | 0.94 | 32 | 9OD |
| 2 | 230 | 0.84 | 0.96 | 30 | 9OD |
| 3 | 78 | 0.30 | 0.73 | 19 | MG |
Interfaces
1 interface between chains.
- A–B · 1383 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3CYZ · Dimeric crystal structure of a pheromone binding protein from Apis mellifera in complex… · 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
- Every structure of UniProt Q9U9J6
- Elsewhere: RCSB PDB 3CYZ · PDBe 3CYZ · UniProt Q9U9J6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.