5D6W: Lysine-specific demethylase 4A

Crystal structure of double tudor domain of human lysine demethylase KDM4A. Determined by X-ray diffraction at 1.99 Å resolution. Released 25 Nov 2015.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,350
Mol. weight: 55.51 kDa
Ligands: SRT
Released: 25 Nov 2015

Explore 5D6W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D6W contains 20 α-helices and 32 β-strands across 4 chains. 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.

Chains A, B, C and D: 5 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	972-990	19	1
β-strand	995-998	4	1
α-helix	1000-1002	3
β-strand	1004	1	1
α-helix	1009-1010	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 4A	A, B, C, D	protein	121	Homo sapiens	O75164 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5D6W_1 Lysine-specific demethylase 4A (chains A, B, C, D)
GSHMALQSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQD
CLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEEL
P

Ligands and cofactors

ID	Name	Formula	Copies
SRT	S,r meso-tartaric acid	C4 H6 O6	4

Primary citation

Reader domain specificity and lysine demethylase-4 family function. Su, Z., Wang, F., Lee, J.H. et al. Nat Commun (2016) 7:13387-13387. DOI 10.1038/ncomms13387 · 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)
5VAR 1.83 Å, Crystal structure of KDM4A tandem TUDOR domain in complex with a tri-methyl lysine…
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

Browse structure collections

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