› 6v2d

X-ray diffraction
2.1Å resolution

Crystal Structure of chromodomain of CDYL2 in complex with inhibitor UNC3866

Released:
DOI: 10.2210/pdb6v2d/pdb
PDB entry 6v2d coloured by chain, front view.
PDB entry 6v2d coloured by chain, side view.
PDB entry 6v2d coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for the Binding Selectivity of Human CDY Chromodomains.
Dong C, Liu Y, Lyu TJ, Beldar S, Lamb KN, Tempel W, Li Y, Li Z, James LI, Qin S, Wang Y, Min J
Cell Chem Biol 27 827-838.e7 (2020)
PMID: 32470319

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-167589 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Chromodomain Y-like protein 2 Chains: A, C, E, G, I, K
Molecule details ›
Chains: A, C, E, G, I, K
Length: 64 amino acids
Theoretical weight: 7.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8N8U2 (Residues: 2-64; Coverage: 13%)
Gene name: CDYL2
Sequence domains: Chromo (CHRromatin Organisation MOdifier) domain
UNC3866 Chains: B, D, F, H, J, L
Molecule details ›
Chains: B, D, F, H, J, L
Length: 6 amino acids
Theoretical weight: 795 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand UNX 28 x UNX
2 modified residues:
Ligand ELY 6 x ELY
Ligand 5R5 6 x 5R5

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E
Spacegroup: P212121
Unit cell:
a: 45.979Å b: 83.835Å c: 115.288Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.212 0.268
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

Chemical tools targeting readers of lysine methylation.
Ortiz et al. (2023)
2 other articles