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Structure of a viral GPCR bound to human chemokine CX3CL1

Analyse Structure of a viral GPCR bound to human chemokine CX3CL1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XT3
Type: protein
Length: 357 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: G-protein coupled receptor homolog US28; Fractalkine
UniProt: P69332, P78423
Ligands: UNL, NAG, PO4
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 64% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	G-protein coupled receptor homolog US28	protein	288	74% helix, 3% strand	P69332
B	Fractalkine	protein	69	20% helix, 25% strand	P78423

Ligands and binding sites

UNL · Unknown ligand · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
PO4 · Phosphate ion · ion · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	655	0.77	0.82	54	empty
2	358	0.66	0.80	37	empty
3	92	0.47	0.81	18	empty
4	56	0.41	0.81	15	empty

Interfaces

1 interface between chains.

A–B · 1229 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).

Compared structures

4XT3 · Structure of a viral GPCR bound to human chemokine CX3CL1 · the same entry in another collection · chain A against A, TM-score 1.00
P78423 · AlphaFold monomer V2.0 prediction for fractalkine (P78423) · 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 P69332
Every structure of UniProt P78423
Elsewhere: RCSB PDB 4XT3 · PDBe 4XT3 · UniProt P69332 · UniProt P78423

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