› 6yke

X-ray diffraction
1.52Å resolution

Crystal structure of YTHDC1 with compound DHU_DC1_038

Released:
DOI: 10.2210/pdb6yke/pdb
PDB 6yke coloured by chain and viewed from the front.
PDB 6yke coloured by chain and viewed from the side.
PDB 6yke coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
Structure-based design of ligands of the m6A-RNA reader YTHDC1
Li Y, Bedi RK, Nai F, von Roten V, Dolbois A, Zalesak F, Nachawati R, Huang D, Caflisch A
Eur J Med Chem Rep 5 100057- (2022)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (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 SO4 10 x SO4
Ligand OUQ 1 x OUQ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 39.29Å b: 103.13Å c: 42.01Å
α: 90° β: 106.126° γ: 90°
R-values:
R R work R free
0.207 0.205 0.232
Expression system: Escherichia coli

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