4O64: Zinc fingers of KDM2B

Zinc fingers of KDM2B. Determined by X-ray diffraction at 2.13 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 2.13 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,791
Mol. weight: 40.84 kDa
Ligands: ZN
Released: 16 Apr 2014

Explore 4O64 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4O64 contains 23 α-helices and 18 β-strands across 3 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 and C: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	611	1	1
α-helix	617-620	4
α-helix	622-623	2
α-helix	628-632	5
α-helix	634-636	3
α-helix	647-649	3
β-strand	655	1	1
α-helix	671-673	3
α-helix	677-682	6
β-strand	686-688	3	2
β-strand	694-695	2	2
α-helix	697-699	3
β-strand	708-709	2	2
β-strand	716-718	3	2

Chain B: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	611	1	3
α-helix	617-620	4
α-helix	622-623	2
α-helix	628-632	5
α-helix	634-636	3
α-helix	647-649	3
β-strand	655	1	3
α-helix	677-682	6
β-strand	686-688	3	4
β-strand	694-695	2	4
α-helix	697-699	3
β-strand	708-709	2	4
β-strand	716-718	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 2B	A, B, C	protein	118	Homo sapiens	Q8NHM5 (AlphaFold model)

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

>4O64_1 Lysine-specific demethylase 2B (chains A, B, C)
GRRRRTRCRKCEACLRTECGECHFCKDMKKFGGPGRMKQSCIMRQCIAPVLPHTAVCLVC
GEAGKEDTVEEEEGKFNLMLMECSICNEIIHPGCLKIKESEGVVNDELPNCWECPKCN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

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

Primary citation

DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants. Xu, C., Liu, K., Lei, M. et al. Structure (2018) 26:85-95.e3. DOI 10.1016/j.str.2017.11.022 · PubMed

Other PDB entries of the same protein (UniProt Q8NHM5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8HCU 2.2 Å, Crystal structure of BCOR/PCGF1/KDM2B complex
5JH5 2.55 Å, Structural Basis for the Hierarchical Assembly of the Core of PRC1.1
6BVA 2.66 Å, Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex.

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