Research workbench
Crystal structure of bovine rhodopsin at 2.6 ångströms resolution
Analyse Crystal structure of bovine rhodopsin at 2.6 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L9H
- Type
- protein
- Length
- 641 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- P02699
- Ligands
- BNG, PLM, HTO, ACE, RET, NAG, MAN, ZN, HG
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 340 | 62% helix, 4% strand | P02699 |
| B | Rhodopsin | protein | 301 | 68% helix, 4% strand | P02699 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 7 copies · chains A, B
- PLM · Palmitic acid · ligand · 5 copies · chains A, B
- HTO · Heptane-1,2,3-triol · ligand · 4 copies · chains A, B
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- RET · Retinal · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B
- ZN · Zinc ion · metal · 7 copies · chains A, B
- HG · Mercury (II) ion · metal · 6 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 | 153 | 0.83 | 0.98 | 31 | RET |
| 2 | 154 | 0.82 | 0.97 | 30 | RET |
| 3 | 707 | 0.68 | 0.76 | 57 | BNG, HG, HTO, PLM |
| 4 | 76 | 0.59 | 0.88 | 15 | HG |
| 5 | 246 | 0.57 | 0.78 | 31 | HTO, PLM |
Interfaces
1 interface between chains.
- A–B · 916 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 lipid, 2 cofactor, 2 covalent, 2 disulfide, 2 glycan (palmitoylation, retinal Schiff base, covalent ligand, disulfide, N-glycosylation).
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 1L9H · PDBe 1L9H · UniProt P02699
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