› 7z8x

X-ray diffraction
1.96Å resolution

Crystal structure of YTHDF2 with compound YLI_DC1_017

Released:
DOI: 10.2210/pdb7z8x/pdb
PDB entry 7z8x coloured by chain, front view.
PDB entry 7z8x coloured by chain, side view.
PDB entry 7z8x 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
OpenAccess logo 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

2 bound ligands:
Ligand IGX 1 x IGX
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P65
Unit cell:
a: 79.82Å b: 79.82Å c: 114.88Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.199 0.197 0.238
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

1 mention without citation

YTHDF1 in Tumor Cell Metabolism: An Updated Review.
Rong et al. (2023)