MolNFT v1 · #148904 · protein
Crystal structure of N2C/D282C stabilized opsin bound to RS15
6FKC · Rhodopsin: “Crystal structure of N2C/D282C stabilized opsin bound to RS15”. X-ray diffraction, 6 ligands (ACE, PLM, DLB), 4 pockets (best druggability 0.82). MolNFT v1 #148904 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6FKC
- 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, DLB, NAG, MAN, BMA
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 326 | 69% helix, 4% strand | P02699 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- PLM · Palmitic acid · ligand · chains A
- DLB · 3-[1'-[(2~{S})-2-(4-chlorophenyl)-3-methyl-butanoyl]spiro[1,3-benzodioxole-2,4'-piperidine]-5-yl]propanoic acid · 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 · 5 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 | 724 | 0.82 | 0.85 | 60 | DLB, BOG |
| 2 | 140 | 0.59 | 0.83 | 23 | BOG |
| 3 | 200 | 0.49 | 0.76 | 23 | empty |
| 4 | 72 | 0.34 | 0.75 | 12 | empty |
Modifications
Observed in the structure: 2 covalent, 2 disulfide, 1 glycan, 1 lipid (disulfide, additive adduct, covalent ligand, N-glycosylation, palmitoylation).
Compared structures
- 6FKC · Crystal structure of N2C/D282C stabilized opsin bound to RS15 · 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 6FKC · PDBe 6FKC · UniProt P02699
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