› 6ynk

X-ray diffraction
1.3Å resolution

Crystal structure of YTHDC1 with compound DHU_DC1_068

Released:
DOI: 10.2210/pdb6ynk/pdb
PDB entry 6ynk coloured by chain, front view.
PDB entry 6ynk coloured by chain, side view.
PDB entry 6ynk coloured by chain, top view.
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:
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

3 bound ligands:
Ligand P0K 2 x P0K
Ligand SO4 8 x SO4
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 39.62Å b: 103.63Å c: 41.96Å
α: 90° β: 104.708° γ: 90°
R-values:
R R work R free
0.179 0.178 0.202
Expression system: Escherichia coli

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