› 5epl

X-ray diffraction
1.81Å resolution

Crystal Structure of chromodomain of CBX4 in complex with inhibitor UNC3866

Released:
DOI: 10.2210/pdb5epl/pdb
PDB entry 5epl coloured by chain, front view.
PDB entry 5epl coloured by chain, side view.
PDB entry 5epl coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1.
Stuckey JI, Dickson BM, Cheng N, Liu Y, Norris JL, Cholensky SH, Tempel W, Qin S, Huber KG, Sagum C, Black K, Li F, Huang XP, Roth BL, Baughman BM, Senisterra G, Pattenden SG, Vedadi M, Brown PJ, Bedford MT, Min J, Arrowsmith CH, James LI, Frye SV
Nat Chem Biol 12 180-7 (2016)
PMID: 26807715

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126208 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 SUMO-protein ligase CBX4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 60 amino acids
Theoretical weight: 7.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O00257 (Residues: 8-65; Coverage: 10%)
Gene name: CBX4
Sequence domains: Chromo (CHRromatin Organisation MOdifier) domain
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
unc3866 Chains: C, D
Molecule details ›
Chains: C, D
Length: 6 amino acids
Theoretical weight: 795 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand UNX 8 x UNX
2 modified residues:
Ligand ELY 2 x ELY
Ligand 5R5 2 x 5R5

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P6122
Unit cell:
a: 65.178Å b: 65.178Å c: 133.057Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.187 0.183 0.216
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

27 review citations

A chemical probe toolbox for dissecting the cancer epigenome.
Shortt et al. (2017)
26 more

2 mentions without citation

A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1.
Stuckey et al. (2016)
1 more