Research workbench
Cryo-EM structure of human ACKR3 in complex with a small molecule partial agonist CCX662, and an intracellular Fab
Analyse Cryo-EM structure of human ACKR3 in complex with a small molecule partial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SK9
- Type
- protein
- Length
- 716 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atypical chemokine receptor 3; CID24 Fab heavy chain; CID24 Fab light chain
- UniProt
- P25106
- Ligands
- CLR, GJ9
- Pockets
- 8 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atypical chemokine receptor 3 | protein | 282 | 81% helix, 3% strand | P25106 |
| F | CID24 Fab heavy chain | protein | 222 | 4% helix, 48% strand | — |
| E | CID24 Fab light chain | protein | 212 | 7% helix, 47% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A
- GJ9 · (1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.80 | 0.96 | 32 | empty |
| 2 | 961 | 0.77 | 0.79 | 47 | GJ9 |
| 3 | 100 | 0.59 | 0.86 | 20 | empty |
| 4 | 312 | 0.52 | 0.74 | 48 | empty |
| 5 | 98 | 0.37 | 0.75 | 23 | empty |
Interfaces
3 interfaces between chains.
- F–E · 1858 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 1568 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 333 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7SK9 · Cryo-EM structure of human ACKR3 in complex with a small molecule partial agonist CCX662… · the same entry in another collection · chain A against A, TM-score 1.00
- P25106 · AlphaFold monomer V2.0 prediction for atypical chemokine receptor 3 (P25106) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P25106
- Elsewhere: RCSB PDB 7SK9 · PDBe 7SK9 · UniProt P25106
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