MolNFT v1 · #47957 · protein
Crystallographic model of 9-cis-rhodopsin
2PED: “Crystallographic model of 9-cis-rhodopsin”. X-ray diffraction, 9 ligands (PLM, ACE, RET), 9 pockets (best druggability 0.83). MolNFT v1 #47957 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2PED
- 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, HTO, NAG, BMA, MAN, ZN, HG
- Pockets
- 9 · best druggability 0.83
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 · 6 copies · chains A, B
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- RET · Retinal · 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 | 164 | 0.83 | 0.98 | 30 | RET |
| 2 | 154 | 0.82 | 0.97 | 31 | RET |
| 3 | 744 | 0.72 | 0.77 | 70 | PLM, HTO, HTG |
| 4 | 866 | 0.70 | 0.75 | 64 | HG, PLM, HTG |
| 5 | 68 | 0.64 | 0.92 | 15 | HG |
Interfaces
1 interface between chains.
- A–B · 785 Ų buried · 3 hydrogen bonds · 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 2PED · PDBe 2PED · UniProt P02699
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.