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Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an intracellular Fab, and an extracellular Fab

Analyse Cryo-EM structure of 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: 7SK4
Type: protein
Length: 831 residues
Chains: 6
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: CLR
Pockets: 13 · best druggability 0.80

Structure

electron microscopy · 6 distinct chains · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Atypical chemokine receptor 3	protein	305	77% helix, 5% strand	P25106
B	Stromal cell-derived factor 1	protein	69	25% helix, 16% strand	P48061
C	CID25 Fab light chain	protein	106	0% helix, 42% strand	—
D	CID25 Fab heavy chain	protein	125	5% helix, 52% strand	—
E	CID24 Fab light chain	protein	101	0% helix, 39% strand	—
F	CID24 Fab heavy chain	protein	125	0% helix, 50% strand	—

Ligands and binding sites

CLR · Cholesterol · ligand · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	164	0.80	0.97	32	empty
2	143	0.77	0.94	31	empty
3	233	0.73	0.88	38	empty
4	100	0.58	0.86	21	empty
5	80	0.47	0.82	20	empty

Interfaces

9 interfaces between chains.

A–B · 2103 Å² buried · 16 hydrogen bonds · protein-protein
A–F · 1545 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 988 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 982 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 942 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

7SK4 · Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an… · 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 7SK4 · PDBe 7SK4 · UniProt P25106 · UniProt P48061

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