Research workbench
The crystal structure of a pheromone binding protein from the cockroach leucophaea maderae in complex with a component of the pheromonal blend: 3-hydroxy-butan-2-one.
Analyse The crystal structure of a pheromone binding protein from the cockroach… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P28
- Type
- protein
- Length
- 236 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pheromone binding protein
- UniProt
- Q8MTC1
- Ligands
- HBS, HBR
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pheromone binding protein | protein | 119 | 70% helix, 2% strand | Q8MTC1 |
| B | Pheromone binding protein | protein | 117 | 67% helix, 2% strand | Q8MTC1 |
Ligands and binding sites
- HBS · S,3-hydroxybutan-2-one · ligand · 2 copies · chains A, B
- HBR · R,3-hydroxybutan-2-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.78 | 0.93 | 25 | HBS, HBR |
| 2 | 180 | 0.66 | 0.85 | 24 | HBS, HBR |
Interfaces
1 interface between chains.
- A–B · 332 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1P28 · The crystal structure of a pheromone binding protein from the cockroach Leucophaea… · 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 Q8MTC1
- Elsewhere: RCSB PDB 1P28 · PDBe 1P28 · UniProt Q8MTC1
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