MolNFT v1 · #158516 · protein
Crystal structure of bovine opsin with beta octyl glucoside bound
6NWE · Rhodopsin: “Crystal structure of bovine opsin with beta octyl glucoside bound”. X-ray diffraction, 4 ligands (PLM, NAG, BMA), 4 pockets (best druggability 0.84). MolNFT v1 #158516 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NWE
- Type
- protein
- Length
- 337 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin; Ilenlkdvglf peptide CT2
- UniProt
- P02699
- Ligands
- PLM, NAG, BMA, SO4
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 326 | 71% helix, 4% strand | P02699 |
| B | Ilenlkdvglf peptide CT2 | protein | 11 | 55% helix, 0% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- 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 | 276 | 0.84 | 0.95 | 43 | BOG |
| 2 | 108 | 0.52 | 0.82 | 20 | empty |
| 3 | 87 | 0.45 | 0.80 | 24 | empty |
| 4 | 57 | 0.33 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 661 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide, 1 glycan, 1 lipid (additive adduct, disulfide, N-glycosylation, palmitoylation).
Compared structures
- 6NWE · Crystal structure of bovine opsin with beta octyl glucoside bound · 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 6NWE · PDBe 6NWE · UniProt P02699
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