9GP4: Lysine-specific demethylase 4A

Jumonji domain-containing protein 2A with crystallization epitope mutations Q953E:A958D. Determined by X-ray diffraction at 1.59 Å resolution. Released 16 Oct 2024.

Method: X-ray diffraction
Resolution: 1.59 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,116
Mol. weight: 13.81 kDa
Released: 16 Oct 2024

Explore 9GP4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GP4 contains 5 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-14	5	1
β-strand	20-38	19	1
β-strand	43-47	5	1
α-helix	49-51	3
β-strand	52	1	1
α-helix	57-60	4
α-helix	62-64	3
β-strand	68-72	5	1
β-strand	78-96	19	1
β-strand	101-105	5	1
α-helix	106-108	3
β-strand	110	1	1
α-helix	115-116	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 4A	A	protein	117	Homo sapiens	O75164 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9GP4_1 Lysine-specific demethylase 4A (chains A)
SMQSITAGQKVISKHKNGAFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLEF
GPPDEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP

Primary citation

A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants. Fairhead, M., Strain-Damerell, C., Ye, M. et al. To be published.

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

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
5D6W 1.99 Å, Crystal structure of double tudor domain of human lysine demethylase KDM4A

Browse structure collections

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