Research workbench
Cryo-EM structure of ACKR3 in complex with CXCL12 and an intracellular Fab
Analyse Cryo-EM structure of ACKR3 in complex with CXCL12 and an intracellular Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SK5
- Type
- protein
- Length
- 897 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atypical chemokine receptor 3; CID24 Fab heavy chain; Stromal cell-derived factor 1…
- UniProt
- P25106, P48061
- Ligands
- CLR
- Pockets
- 13 · best druggability 0.79
Structure
electron microscopy · 5 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atypical chemokine receptor 3 | protein | 300 | 78% helix, 6% strand | P25106 |
| F | CID24 Fab heavy chain | protein | 220 | 3% helix, 49% strand | — |
| B | Stromal cell-derived factor 1 | protein | 63 | 11% helix, 33% strand | P48061 |
| E | CID24 Fab light chain | protein | 211 | 5% helix, 45% strand | — |
| K | Anti-Fab nanobody | protein | 103 | 3% helix, 45% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 7 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.79 | 0.96 | 29 | empty |
| 2 | 114 | 0.74 | 0.94 | 24 | empty |
| 3 | 118 | 0.72 | 0.93 | 27 | empty |
| 4 | 247 | 0.70 | 0.85 | 39 | empty |
| 5 | 239 | 0.65 | 0.83 | 37 | empty |
Interfaces
5 interfaces between chains.
- F–E · 1781 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 1574 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1535 Ų buried · 10 hydrogen bonds · protein-protein
- E–K · 657 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 317 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7SK5 · Cryo-EM structure of ACKR3 in complex with CXCL12 and an intracellular Fab · the same entry in another collection · chain F against F, 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 0.93
- 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 0.78
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 7SK5 · PDBe 7SK5 · UniProt P25106 · UniProt P48061
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