Research workbench
Crystal structure of bos taurus opsin at 2.7 ångström
Analyse Crystal structure of bos taurus opsin at 2.7 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TE3
- Type
- protein
- Length
- 326 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- P02699
- Ligands
- PLM, NAG, BMA, MAN, SO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 326 | 70% helix, 4% strand | P02699 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 2 copies · chains A
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.84 | 0.95 | 37 | BOG |
| 2 | 261 | 0.58 | 0.78 | 27 | empty |
| 3 | 68 | 0.53 | 0.87 | 17 | empty |
| 4 | 103 | 0.51 | 0.82 | 19 | empty |
| 5 | 51 | 0.45 | 0.84 | 20 | empty |
Modifications
Observed in the structure: 2 lipid, 1 disulfide, 1 glycan (palmitoylation, 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 5TE3 · PDBe 5TE3 · UniProt P02699
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.