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Dimeric crystal structure of a pheromone binding protein mutant D35N, from apis mellifera, at pH 7.0
Analyse Dimeric crystal structure of a pheromone binding protein mutant D35N, from apis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D78
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pheromone-binding protein ASP1
- UniProt
- Q9U9J6
- Ligands
- NBB
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pheromone-binding protein ASP1 | protein | 119 | 62% helix, 2% strand | Q9U9J6 |
Ligands and binding sites
- NBB · N-butyl-benzenesulfonamide · ligand · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.85 | 0.95 | 31 | NBB, EDO |
| 2 | 257 | 0.81 | 0.93 | 22 | NBB |
| 3 | 106 | 0.50 | 0.81 | 27 | empty |
| 4 | 83 | 0.43 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 489 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3D78 · Dimeric crystal structure of a pheromone binding protein mutant D35N, from apis… · 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 3D78 · PDBe 3D78 · UniProt Q9U9J6
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