Research workbench
X-ray crystal structure of visual arrestin complexed with inositol 1, 4,5-triphosphate
Analyse X-ray crystal structure of visual arrestin complexed with inositol 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F1X
- Type
- protein
- Length
- 1,453 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-arrestin
- UniProt
- P08168
- Ligands
- I3P, PTD
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-arrestin | protein | 364 | 7% helix, 49% strand | P08168 |
| B | S-arrestin | protein | 365 | 4% helix, 50% strand | P08168 |
| C | S-arrestin | protein | 359 | 6% helix, 48% strand | P08168 |
| D | S-arrestin | protein | 365 | 6% helix, 49% strand | P08168 |
Ligands and binding sites
- I3P · D-myo-inositol-1,4,5-triphosphate · ligand · 4 copies · chains A, B, C, D
- PTD · Pentanedial · ligand · 3 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.74 | 0.80 | 77 | empty |
| 2 | 1183 | 0.73 | 0.77 | 100 | empty |
| 3 | 92 | 0.59 | 0.88 | 32 | empty |
| 4 | 133 | 0.56 | 0.83 | 21 | I3P |
| 5 | 100 | 0.56 | 0.85 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1238 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1070 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 633 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 630 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7F1X · X-ray crystal structure of visual arrestin complexed with inositol 1,4,5-triphosphate · the same entry in another collection · chain D against D, TM-score 1.00
- P08168 · AlphaFold monomer V2.0 prediction for S-arrestin (P08168) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P08168
- Elsewhere: RCSB PDB 7F1X · PDBe 7F1X · UniProt P08168
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