MolNFT v1 · #160328 · protein
Crystal structure of bovine opsin with nerol bound
6PH7 · Rhodopsin: “Crystal structure of bovine opsin with nerol bound”. X-ray diffraction, 4 ligands (PLM, NZZ, NAG), 3 pockets (best druggability 0.84). MolNFT v1 #160328 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PH7
- Type
- protein
- Length
- 337 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin; G protein CT2 peptide
- UniProt
- P02699
- Ligands
- PLM, NZZ, NAG, BMA
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 326 | 71% helix, 4% strand | P02699 |
| B | G protein CT2 peptide | protein | 11 | 55% helix, 0% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- NZZ · (2Z)-3,7-dimethylocta-2,6-dien-1-ol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- BOG · octyl beta-D-glucopyranoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.84 | 0.94 | 35 | NZZ |
| 2 | 129 | 0.53 | 0.81 | 20 | empty |
| 3 | 68 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 675 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 glycan, 1 lipid (disulfide, N-glycosylation, palmitoylation).
Compared structures
- 6PH7 · Crystal structure of bovine opsin with nerol 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 6PH7 · PDBe 6PH7 · UniProt P02699
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