Research workbench
Crystal structure of N2C/D282C stabilized opsin bound to RS08
Analyse Crystal structure of N2C/D282C stabilized opsin bound to RS08 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FK8
- Type
- protein
- Length
- 326 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- P02699
- Ligands
- ACE, PLM, DNZ, NAG, MAN, BMA
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 326 | 67% helix, 4% strand | P02699 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- PLM · Palmitic acid · ligand · chains A
- DNZ · (2~{R},3~{S})-3-azanyl-2-(4-chlorophenyl)-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.83 | 0.86 | 63 | DNZ, BOG |
| 2 | 99 | 0.57 | 0.85 | 20 | empty |
| 3 | 213 | 0.50 | 0.75 | 29 | empty |
| 4 | 63 | 0.32 | 0.75 | 10 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 covalent, 1 glycan, 1 lipid (disulfide, covalent ligand, N-glycosylation, palmitoylation).
Compared structures
- 6FK8 · Crystal structure of N2C/D282C stabilized opsin bound to RS08 · 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 P02699
- Elsewhere: RCSB PDB 6FK8 · PDBe 6FK8 · UniProt P02699
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