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JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41)

X-ray diffraction
2.32Å resolution
PDB entry 2ybs coloured by chain, front view.
PDB entry 2ybs coloured by chain, side view.
PDB entry 2ybs coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero dimer (preferred)
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Lysine-specific demethylase 4A and Histone H3.1t
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Multimeric state: hetero dimer
Accessible surface area: 15978.19 Å2
Buried surface area: 2177.17 Å2
Dissociation area: 931.15 Å2
Dissociation energy (ΔGdiss): 5.43 kcal/mol
Dissociation entropy (TΔSdiss): 8.2 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-130874
Assembly 2
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Assembly Name: Lysine-specific demethylase 4A and Histone H3.1t
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Multimeric state: hetero dimer
Accessible surface area: 15776.22 Å2
Buried surface area: 2070.66 Å2
Dissociation area: 984.92 Å2
Dissociation energy (ΔGdiss): 6.9 kcal/mol
Dissociation entropy (TΔSdiss): 8.18 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-130874

Macromolecules

Lysine-specific demethylase 4A
Chains: A, B
Length: 381 amino acids
Theoretical weight: 44.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75164 (Residues: 1-359; Coverage: 34%)
Gene names: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677
Pfam:
InterPro:
CATH: Cupin
Lysine-specific demethylase 4A in PDB entry 2ybs, assembly 1, front view.
Lysine-specific demethylase 4A in PDB entry 2ybs, assembly 1, side view.
Lysine-specific demethylase 4A in PDB entry 2ybs, assembly 1, top view.
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Histone H3.1t
Chains: C, D
Length: 12 amino acids
Theoretical weight: 1.36 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q16695 (Residues: 31-42; Coverage: 9%)
Gene names: H3-4, H3FT, HIST3H3
Histone H3.1t in PDB entry 2ybs, assembly 1, front view.
Histone H3.1t in PDB entry 2ybs, assembly 1, side view.
Histone H3.1t in PDB entry 2ybs, assembly 1, top view.
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