5VAR: KDM4A tandem TUDOR domain

Crystal structure of KDM4A tandem TUDOR domain in complex with a tri-methyl lysine competitive inhibitor. Determined by X-ray diffraction at 1.83 Å resolution. Released 28 Mar 2018.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 1
Atoms: 961
Mol. weight: 13.79 kDa
Ligands: 92Y
Released: 28 Mar 2018

Explore 5VAR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VAR contains 4 α-helices and 8 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	904-908	5	1
β-strand	914-932	19	1
β-strand	937-941	5	1
α-helix	943-945	3
β-strand	946	1	1
α-helix	951-954	4
α-helix	956-958	3
β-strand	962-966	5	1
β-strand	972-989	18	1
β-strand	995-998	4	1
α-helix	1000-1002	3
β-strand	1003	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 4A	A	protein	119	Homo sapiens	O75164 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5VAR_1 Lysine-specific demethylase 4A (chains A)
GSHMQSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCL
QFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP

Ligands and cofactors

ID	Name	Formula	Copies
92Y	(1R,2S,3R,4S)-3-[(dimethylamino)methyl]-1-phenylbicyclo[2.2.1]heptan-2-ol	C16 H23 N O	1

Primary citation

Targeting lysine specific demethylase 4A (KDM4A) tandem TUDOR domain - A fragment based approach. Upadhyay, A.K., Judge, R.A., Li, L. et al. Bioorg Med Chem Lett (2018) 28:1708-1713. DOI 10.1016/j.bmcl.2018.04.050 · PubMed

Other PDB entries of the same protein (UniProt O75164 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GP4 1.59 Å, Jumonji domain-containing protein 2A with crystallization epitope mutations Q953E:A958D
9GII 1.7 Å, Jumonji domain-containing protein 2A with crystallization epitope mutation R913A
6G5X 1.78 Å, Crystal Structure of KDM4A with compound YP-02-145
2QQR 1.8 Å, JMJD2A hybrid tudor domains
4V2W 1.81 Å, JMJD2A complexed with ni(ii), nog and histone H3K27me3 peptide (16-35)
6G5W 1.83 Å, Crystal Structure of KDM4A with compound YP-03-038
9GLE 1.88 Å, Jumonji domain-containing protein 2A with crystallization epitope mutations A91T:T93S
2OX0 1.95 Å, Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9
6H8P 1.98 Å, JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)
3PDQ 1.99 Å, Crystal structure of JMJD2A complexed with bipyridyl inhibitor
2P5B 1.99 Å, The complex structure of JMJD2A and trimethylated H3K36 peptide
5D6W 1.99 Å, Crystal structure of double tudor domain of human lysine demethylase KDM4A

Browse structure collections

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