Research workbench
Crystal structure of a rhodopsin stabilizing mutant expressed in mammalian cells
Analyse Crystal structure of a rhodopsin stabilizing mutant expressed in mammalian cells in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J4Y
- Type
- protein
- Length
- 652 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- P02699
- Ligands
- ACE, RET, NAG
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rhodopsin | protein | 326 | 56% helix, 2% strand | P02699 |
Ligands and binding sites
- 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 · 2 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.82 | 0.97 | 30 | RET |
| 2 | 161 | 0.82 | 0.97 | 28 | RET |
| 3 | 332 | 0.60 | 0.77 | 47 | empty |
| 4 | 298 | 0.56 | 0.76 | 46 | empty |
| 5 | 168 | 0.55 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1000 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 cofactor, 2 covalent, 2 glycan (disulfide, retinal Schiff base, covalent ligand, N-glycosylation).
Compared structures
- 2J4Y · Crystal structure of a rhodopsin stabilizing mutant expressed in mammalian cells · the same entry in another collection · chain A against A, TM-score 1.00
- P02699 · AlphaFold monomer V2.0 prediction for rhodopsin (P02699) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 2J4Y · PDBe 2J4Y · UniProt P02699
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