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Crystal structure of an agonist bound GPCR
Analyse Crystal structure of an agonist bound GPCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KPC
- Type
- protein
- Length
- 445 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Enterobacteria phage RB59; Homo sapiens
- Molecule
- Cannabinoid receptor 2,Endolysin
- EC
- 3.2.1.17
- UniProt
- P34972, A0A097J809
- Ligands
- E3R
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · resolution 3.2 · 1 distinct chain · 71% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cannabinoid receptor 2,Endolysin (EC 3.2.1.17) | protein | 445 | 71% helix, 3% strand | P34972, A0A097J809 |
Ligands and binding sites
- E3R · 7-[(6aR,9R,10aR)-1-Hydroxy-9-(hydroxymethyl)-6,6-dimethyl-6a,7,8,9,10,10a-hexahydro-6H-benzo[c]chromen-3-yl]- 7-methyloctanenitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.85 | 0.96 | 32 | E3R |
| 2 | 172 | 0.42 | 0.74 | 26 | empty |
| 3 | 63 | 0.36 | 0.77 | 14 | empty |
| 4 | 81 | 0.34 | 0.74 | 15 | empty |
| 5 | 60 | 0.29 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 P34972
- Every structure of UniProt A0A097J809
- Elsewhere: RCSB PDB 6KPC · PDBe 6KPC · UniProt P34972 · UniProt A0A097J809
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