MolNFT v1 · #117121 · protein
Crystal structure of T94I rhodopsin mutant
5DYS: “Crystal structure of T94I rhodopsin mutant”. X-ray diffraction, 7 ligands (PLM, ACE, RET), 5 pockets (best druggability 0.84). MolNFT v1 #117121 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DYS
- 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, ACE, RET, 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
- ACE · Acetyl group · ligand · chains A
- RET · Retinal · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- BOG · octyl beta-D-glucopyranoside · additive · 2 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 | 235 | 0.84 | 0.96 | 30 | RET |
| 2 | 117 | 0.56 | 0.83 | 21 | empty |
| 3 | 124 | 0.53 | 0.82 | 26 | empty |
| 4 | 255 | 0.52 | 0.75 | 26 | empty |
| 5 | 66 | 0.33 | 0.75 | 11 | empty |
Modifications
Observed in the structure: 2 disulfide, 2 lipid, 1 cofactor, 1 covalent, 1 glycan (disulfide, palmitoylation, retinal Schiff base, covalent ligand, 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 5DYS · PDBe 5DYS · UniProt P02699
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