Research workbench
Cryo-EM structure of human ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ and an intracellular Fab
Analyse Cryo-EM structure of human ACKR3 in complex with chemokine N-terminal mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SK6
- Type
- protein
- Length
- 585 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atypical chemokine receptor 3; Stromal cell-derived factor 1; CID24 Fab light chain…
- UniProt
- P25106, P48061
- Pockets
- 4 · best druggability 0.76
Structure
electron microscopy · 4 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atypical chemokine receptor 3 | protein | 300 | 78% helix, 4% strand | P25106 |
| B | Stromal cell-derived factor 1 | protein | 59 | 22% helix, 25% strand | P48061 |
| E | CID24 Fab light chain | protein | 101 | 0% helix, 40% strand | — |
| F | CID24 Fab heavy chain | protein | 125 | 2% helix, 50% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.76 | 0.89 | 44 | empty |
| 2 | 100 | 0.75 | 0.96 | 17 | empty |
| 3 | 63 | 0.48 | 0.85 | 15 | empty |
| 4 | 171 | 0.47 | 0.75 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2016 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 1538 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1026 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 309 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7SK6 · Cryo-EM structure of human ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ… · 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 0.92
- 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 0.64
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 7SK6 · PDBe 7SK6 · UniProt P25106 · UniProt P48061
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