› 3odu

X-ray diffraction
2.5Å resolution

The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1t

Released:
DOI: 10.2210/pdb3odu/pdb
PDB entry 3odu coloured by chain, front view.
PDB entry 3odu coloured by chain, side view.
PDB entry 3odu coloured by chain, top view.
Source organisms:
Primary publication:
Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists.
Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC
Science 330 1066-71 (2010)
PMID: 20929726

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132998 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
C-X-C chemokine receptor type 4; Endolysin Chains: A, B
Molecule details ›
Chains: A, B
Length: 502 amino acids
Theoretical weight: 56.96 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P61073 (Residues: 2-229, 230-319; Coverage: 90%)
  • Canonical: P00720 (Residues: 2-161; Coverage: 98%)
Gene names: CXCR4, E
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ITD 2 x ITD
Ligand OLC 5 x OLC
Ligand OLA 6 x OLA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21
Unit cell:
a: 64.54Å b: 83.692Å c: 119.995Å
α: 90° β: 102.17° γ: 90°
R-values:
R R work R free
0.24 0.237 0.282
Expression system: Spodoptera frugiperda

Quick links

Citations

234 review citations

Molecular signatures of G-protein-coupled receptors.
Venkatakrishnan et al. (2013)
233 more

276 mentions without citation

Structure-function of the G protein-coupled receptor superfamily.
Katritch et al. (2013)
275 more