› 7z7b

X-ray diffraction
1.8Å resolution

Crystal structure of YTHDF2 with compound YLI_DC1_003

Released:
DOI: 10.2210/pdb7z7b/pdb
PDB entry 7z7b coloured by chain, front view.
PDB entry 7z7b coloured by chain, side view.
PDB entry 7z7b coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Fragment Ligands of the m6A-RNA Reader YTHDF2.
Nai F, Nachawati R, Zálešák F, Wang X, Li Y, Caflisch A
ACS Med Chem Lett 13 1500-1509 (2022)
PMID: 36110386

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195267 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
YTH domain-containing family protein 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 167 amino acids
Theoretical weight: 19.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y5A9 (Residues: 408-552; Coverage: 25%)
Gene names: HGRG8, YTHDF2
Sequence domains: YT521-B-like domain

Ligands and Environments

4 bound ligands:
Ligand SO4 6 x SO4
Ligand CL 4 x CL
Ligand OYK 2 x OYK
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P65
Unit cell:
a: 80.38Å b: 80.38Å c: 113.44Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.209 0.178 0.193
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Characterization of epitranscriptome reader proteins experimentally and in silico: Current knowledge and future perspectives beyond the YTH domain.
Miller et al. (2023)
2 other articles