Research workbench
Crystal structure of rhodopsin bound to visual arrestin
Analyse Crystal structure of rhodopsin bound to visual arrestin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DGY
- Type
- protein
- Length
- 3,128 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ENDOLYSIN,RHODOPSIN,S-arrestin
- EC
- 3.2.1.17
- UniProt
- P00720, P08100, P20443
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | ENDOLYSIN,RHODOPSIN,S-arrestin (EC 3.2.1.17) | protein | 833 | 42% helix, 22% strand | P00720, P08100, P20443 |
| B | ENDOLYSIN,RHODOPSIN,S-arrestin (EC 3.2.1.17) | protein | 673 | 36% helix, 25% strand | P00720, P08100, P20443 |
| C | ENDOLYSIN,RHODOPSIN,S-arrestin (EC 3.2.1.17) | protein | 789 | 42% helix, 22% strand | P00720, P08100, P20443 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.86 | 0.96 | 39 | empty |
| 2 | 311 | 0.84 | 0.94 | 44 | empty |
| 3 | 293 | 0.83 | 0.93 | 44 | empty |
| 4 | 282 | 0.83 | 0.93 | 41 | empty |
| 5 | 892 | 0.74 | 0.78 | 92 | empty |
Interfaces
3 interfaces between chains.
- B–D · 522 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 464 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 412 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5DGY · Crystal structure of rhodopsin bound to visual arrestin · the same entry in another collection · chain C against C, TM-score 1.00
- P20443 · AlphaFold monomer V2.0 prediction for S-arrestin (P20443) · a predicted model of the same protein · chain B against A, TM-score 0.50
- P08100 · AlphaFold monomer V2.0 prediction for rhodopsin (P08100) · a predicted model of the same protein · chain B against A, TM-score 0.48
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 P00720
- Every structure of UniProt P08100
- Every structure of UniProt P20443
- Elsewhere: RCSB PDB 5DGY · PDBe 5DGY · UniProt P00720 · UniProt P08100 · UniProt P20443
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