Research workbench
Crystal structure of odorant binding protein 1 (AaegOBP1) from Aedes aegypti
Analyse Crystal structure of odorant binding protein 1 (AaegOBP1) from Aedes aegypti in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K1E
- Type
- protein
- Length
- 240 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Aedes aegypti
- Molecule
- Odorant binding protein
- UniProt
- Q6Y2R8
- Ligands
- PEU, MG, CL
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · resolution 1.85 · 2 distinct chains · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Odorant binding protein | protein | 124 | 59% helix, 2% strand | Q6Y2R8 |
| B | Odorant binding protein | protein | 116 | 63% helix, 2% strand | Q6Y2R8 |
Ligands and binding sites
- PEU · 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56, 59,62,65,68,71,74,77,80-heptacosaoxadooctacontan-82-ol · ligand · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
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 | 484 | 0.87 | 0.93 | 67 | PEU |
| 2 | 160 | 0.51 | 0.78 | 31 | empty |
| 3 | 56 | 0.27 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 724 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3K1E · Crystal structure of odorant binding protein 1 (AAEGOBP1) from aedes aegypti · 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 Q6Y2R8
- Elsewhere: RCSB PDB 3K1E · PDBe 3K1E · UniProt Q6Y2R8
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