Research workbench
Porcine odorant binding protein complexed with pyrazine (2-isobutyl-3-metoxypyrazine)
Analyse Porcine odorant binding protein complexed with pyrazine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DZK
- Type
- protein
- Length
- 296 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Odorant-binding protein
- UniProt
- P81245
- Ligands
- PRZ
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Odorant-binding protein | protein | 148 | 17% helix, 50% strand | P81245 |
Ligands and binding sites
- PRZ · 2-isobutyl-3-methoxypyrazine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.85 | 0.99 | 22 | PRZ |
| 2 | 167 | 0.85 | 0.99 | 22 | PRZ |
| 3 | 321 | 0.65 | 0.81 | 45 | empty |
| 4 | 129 | 0.48 | 0.79 | 22 | empty |
| 5 | 51 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 850 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1DZK · Porcine Odorant Binding Protein Complexed with pyrazine (2-isobutyl-3-metoxypyrazine) · the same entry in another collection · chain A against A, TM-score 1.00
- P81245 · AlphaFold monomer V2.0 prediction for odorant-binding protein (P81245) · a predicted model of the same protein · chain A 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 P81245
- Elsewhere: RCSB PDB 1DZK · PDBe 1DZK · UniProt P81245
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