4BBQ: Lysine-specific demethylase 2A

Crystal structure of the CXXC and PHD domain of Human Lysine-specific Demethylase 2A (KDM2A)(FBXL11). Determined by X-ray diffraction at 2.24 Å resolution. Released 10 Oct 2012.

Method: X-ray diffraction
Resolution: 2.24 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 1,682
Mol. weight: 27.22 kDa
Ligands: ZN
Released: 10 Oct 2012

Explore 4BBQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BBQ contains 20 α-helices and 16 β-strands across 2 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.

Chain A: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	569	1	1
α-helix	575-578	4
α-helix	580-581	2
α-helix	586-590	5
α-helix	592-594	3
α-helix	602-604	3
α-helix	605-607	3
α-helix	612	1
β-strand	613	1	1
α-helix	614-615	2
β-strand	619	1	2
α-helix	625	1
β-strand	626	1	2
α-helix	627	1
α-helix	629-632	4
α-helix	635-637	3
β-strand	640-642	3	3
β-strand	648-649	2	3
α-helix	651-653	3
β-strand	661-662	2	3
β-strand	669-671	3	3

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	569	1	4
α-helix	575-578	4
α-helix	580-581	2
α-helix	586-590	5
α-helix	592-594	3
α-helix	602-604	3
α-helix	605-607	3
β-strand	613	1	4
β-strand	619	1	5
β-strand	626	1	5
β-strand	640-642	3	6
β-strand	648-649	2	6
α-helix	651-653	3
β-strand	661-662	2	6
β-strand	669-671	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 2A	A, B	protein	117	HOMO SAPIENS	Q9Y2K7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4BBQ_1 LYSINE-SPECIFIC DEMETHYLASE 2A (chains A, B)
SMRRVRCRKCKACVQGECGVCHYCRDMKKFGGPGRMKQSCVLRQCLAPRLPHSVTCSLCG
EVDQNEETQDFEKKLMECCICNEIVHPGCLQMDGEGLLNEELPNCWECPKCYQEDSS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Water and common crystallization additives (EDO) are not listed.

Primary citation

Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (Kdm2A)(Fbxl11). Allerston, C.K., Watson, A.A., Edlich, C. et al. To be published.

Other PDB entries of the same protein (UniProt Q9Y2K7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PHV 2.16 Å, Crystal structure of human KDM2A with substrate competitive inhibitor 183c
6BYH 2.61 Å, Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex.
2YU1 2.7 Å, Crystal structure of hJHDM1A complexed with a-ketoglutarate
2YU2 2.7 Å, Crystal structure of hJHDM1A without a-ketoglutarate
7UV9 3.2 Å, KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate
6C16 3.27 Å, Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex.

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