› 2ypd

X-ray diffraction
2.1Å resolution

Crystal structure of the Jumonji domain of human Jumonji domain containing 1C protein

Released:
DOI: 10.2210/pdb2ypd/pdb
PDB entry 2ypd coloured by chain, front view.
PDB entry 2ypd coloured by chain, side view.
PDB entry 2ypd coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Vollmar M, Johansson C, Krojer T, Berridge G, Burgess-Brown N, Strain-Damerell C, Froese S, Williams E, Goubin S, Coutandin D, von Delft F, Arrowsmith CH, Bountra C, Edwards A, Oppermann U

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-172367 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable JmjC domain-containing histone demethylation protein 2C Chains: A, B
Molecule details ›
Chains: A, B
Length: 392 amino acids
Theoretical weight: 45.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q15652 (Residues: 2157-2540; Coverage: 15%)
Gene names: JHDM2C, JMJD1C, KIAA1380, TRIP8
Sequence domains: JmjC domain, hydroxylase
Structure domains: Cupin

Ligands and Environments

2 bound ligands:
Ligand EMT 11 x EMT
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Unit cell:
a: 45.718Å b: 112.206Å c: 165.173Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.215 0.24
Expression system: Escherichia coli BL21(DE3)

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