MolNFT v1 · #73731 · protein
Crystal structure of bovine rhodopsin with beta-ionone
3OAX: “Crystal structure of bovine rhodopsin with beta-ionone”. X-ray diffraction, 11 ligands (PLM, ACE, RET), 9 pockets (best druggability 0.82). MolNFT v1 #73731 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OAX
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- P02699
- Ligands
- PLM, ACE, RET, 4E6, ID3, HTO, NAG, BMA, MAN, ZN, HG
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rhodopsin | protein | 348 | 62% helix, 3% strand | P02699 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 4 copies · chains A, B
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- RET · Retinal · ligand · 2 copies · chains A, B
- 4E6 · (4E,6E)-hexadeca-1,4,6-triene · ligand · 2 copies · chains A, B
- ID3 · (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one · ligand · 2 copies · chains A, B
- HTO · Heptane-1,2,3-triol · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 7 copies · chains A, B
- HG · Mercury (II) ion · metal · 6 copies · chains A, B
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.82 | 0.98 | 29 | RET |
| 2 | 148 | 0.81 | 0.97 | 31 | RET |
| 3 | 1152 | 0.72 | 0.75 | 90 | HG, 4E6, HTG |
| 4 | 75 | 0.63 | 0.90 | 20 | HG |
| 5 | 302 | 0.62 | 0.79 | 36 | PLM |
Interfaces
1 interface between chains.
- A–B · 762 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 glycan, 4 lipid, 2 cofactor, 2 covalent, 2 disulfide (N-glycosylation, palmitoylation, retinal Schiff base, covalent ligand, 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 P02699
- Elsewhere: RCSB PDB 3OAX · PDBe 3OAX · UniProt P02699
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