Research workbench
Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, and an extracellular Fab
Analyse Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SK7
- Type
- protein
- Length
- 854 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atypical chemokine receptor 3; Stromal cell-derived factor 1; CID25 Fab light chain…
- UniProt
- P25106, P48061
- Ligands
- GJ9, CLR
- Pockets
- 11 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atypical chemokine receptor 3 | protein | 267 | 77% helix, 6% strand | P25106 |
| B | Stromal cell-derived factor 1 | protein | 62 | 18% helix, 34% strand | P48061 |
| C | CID25 Fab light chain | protein | 211 | 6% helix, 47% strand | — |
| D | CID25 Fab heavy chain | protein | 211 | 3% helix, 50% strand | — |
| K | Anti-Fab nanobody | protein | 103 | 3% helix, 41% strand | — |
Ligands and binding sites
- 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
- CLR · Cholesterol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.85 | 0.86 | 59 | GJ9 |
| 2 | 176 | 0.69 | 0.88 | 24 | empty |
| 3 | 221 | 0.52 | 0.76 | 33 | empty |
| 4 | 89 | 0.52 | 0.84 | 22 | empty |
| 5 | 69 | 0.48 | 0.84 | 24 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1787 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1386 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 983 Ų buried · 9 hydrogen bonds · protein-protein
- C–K · 683 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 681 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7SK7 · Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist… · the same entry in another collection · chain B against B, 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 0.94
- P48061 · AlphaFold monomer V2.0 prediction for stromal cell-derived factor 1 (P48061) · a predicted model of the same protein · chain B against A, TM-score 0.87
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
- Every structure of UniProt P48061
- Elsewhere: RCSB PDB 7SK7 · PDBe 7SK7 · UniProt P25106 · UniProt P48061
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