MolNFT v1 · #18026 · protein
Complex of bovine odorant binding protein (obp) with a selenium containing odorant
1PBO: “Complex of bovine odorant binding protein (obp) with a selenium containing odorant”. X-ray diffraction, 1 ligand (SES), 4 pockets (best druggability 0.84). MolNFT v1 #18026 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1PBO
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Odorant binding protein
- UniProt
- P07435
- Ligands
- SES
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Odorant binding protein | protein | 157 | 18% helix, 47% strand | P07435 |
| B | Odorant binding protein | protein | 151 | 15% helix, 48% strand | P07435 |
Ligands and binding sites
- SES · 4-butyl-5-propyl-1,3-selenazol-2-amine · ligand · 2 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 | 178 | 0.84 | 0.98 | 26 | SES |
| 2 | 176 | 0.84 | 0.98 | 25 | SES |
| 3 | 233 | 0.77 | 0.91 | 28 | empty |
| 4 | 123 | 0.39 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2477 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1PBO · Complex of bovine odorant binding protein (obp) with a selenium containing odorant · the same entry in another collection · chain A against A, TM-score 1.00
- P07435 · AlphaFold monomer V2.0 prediction for odorant-binding protein (P07435) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P07435
- Elsewhere: RCSB PDB 1PBO · PDBe 1PBO · UniProt P07435
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