MolNFT v1 · #137830 · protein
Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser
5W0P · ENDOLYSIN,RHODOPSIN,S-arrestin: “Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.81). MolNFT v1 #137830 on…
- PDB
- 5W0P
- Type
- protein
- Length
- 3,277 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
- A0A097J792, P08100, P20443
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ENDOLYSIN,RHODOPSIN,S-arrestin (EC 3.2.1.17) | protein | 849 | 42% helix, 23% strand | A0A097J792, P08100, P20443 |
| B | ENDOLYSIN,RHODOPSIN,S-arrestin (EC 3.2.1.17) | protein | 804 | 43% helix, 23% strand | A0A097J792, P08100, P20443 |
| C | ENDOLYSIN,RHODOPSIN,S-arrestin (EC 3.2.1.17) | protein | 850 | 42% helix, 24% strand | A0A097J792, P08100, P20443 |
| D | ENDOLYSIN,RHODOPSIN,S-arrestin (EC 3.2.1.17) | protein | 774 | 41% helix, 24% strand | A0A097J792, P08100, P20443 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 239 | 0.81 | 0.94 | 44 | empty |
| 2 | 153 | 0.81 | 0.97 | 34 | empty |
| 3 | 168 | 0.81 | 0.96 | 37 | empty |
| 4 | 136 | 0.79 | 0.96 | 31 | empty |
| 5 | 824 | 0.73 | 0.78 | 77 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1205 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1137 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 578 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 431 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 modified, 4 glycan (disulfide, phosphorylation, N-glycosylation).
Compared structures
- 5W0P · Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron… · the same entry in another collection · chain A against A, TM-score 1.00
- P20443 · AlphaFold monomer V2.0 prediction for S-arrestin (P20443) · a predicted model of the same protein · chain D against A, TM-score 0.44
- P08100 · AlphaFold monomer V2.0 prediction for rhodopsin (P08100) · a predicted model of the same protein · chain D against A, TM-score 0.42
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 A0A097J792
- Every structure of UniProt P08100
- Every structure of UniProt P20443
- Elsewhere: RCSB PDB 5W0P · PDBe 5W0P · UniProt A0A097J792 · UniProt P08100 · UniProt P20443
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