› 6t09

X-ray diffraction
1.75Å resolution

Crystal structure of YTHDC1 with fragment 24 (PSI_DC1_003)

Released:
DOI: 10.2210/pdb6t09/pdb
PDB entry 6t09 coloured by chain, front view.
PDB entry 6t09 coloured by chain, side view.
PDB entry 6t09 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Selectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments.
Bedi RK, Huang D, Wiedmer L, Li Y, Dolbois A, Wojdyla JA, Sharpe ME, Caflisch A, Sledz P
ACS Chem Biol 15 618-625 (2020)
PMID: 32101404

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-572483 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
YTH domain-containing protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 183 amino acids
Theoretical weight: 20.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96MU7 (Residues: 345-509; Coverage: 23%)
Gene names: KIAA1966, YT521, YTHDC1
Sequence domains: YT521-B-like domain

Ligands and Environments

2 bound ligands:
Ligand M4T 2 x M4T
Ligand SO4 7 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 39.668Å b: 103.261Å c: 42.138Å
α: 90° β: 105.561° γ: 90°
R-values:
R R work R free
0.19 0.188 0.225
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Targeting the RNA demethylase FTO for cancer therapy.
Zhou et al. (2021)
1 more