4MN3: Chromobox protein homolog 7

Chromodomain antagonists that target the polycomb-group methyllysine reader protein Chromobox homolog 7 (CBX7). Determined by X-ray diffraction at 1.54 Å resolution. Released 2 Apr 2014.

Method: X-ray diffraction
Resolution: 1.54 Å
Organisms: Homo sapiens, Synthetic peptide
Chains: 2
Atoms: 597
Mol. weight: 8.04 kDa
Ligands: MG, P33
Released: 2 Apr 2014

Explore 4MN3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4MN3 contains 3 α-helices and 6 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: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	7-16	10	2
β-strand	19-26	8	2
α-helix	31-33	3
β-strand	35-38	4	2
α-helix	39-41	3
β-strand	42	1	1
α-helix	45-54	10

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromobox protein homolog 7	A	protein	56	Homo sapiens	O95931 (AlphaFold model)
peptide	B	protein	7	Synthetic peptide

Sequence of entity 1 (A), FASTA

>4MN3_1 Chromobox protein homolog 7 (chains A)
GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE

Sequence of entity 2 (B), FASTA

>4MN3_2 peptide (chains B)
XFAYKSX

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
P33	3,6,9,12,15,18-hexaoxaicosane-1,20-diol	C14 H30 O8	1

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

Primary citation

Chromodomain Antagonists That Target the Polycomb-Group Methyllysine Reader Protein Chromobox Homolog 7 (CBX7). Simhadri, C., Daze, K.D., Douglas, S.F. et al. J Med Chem (2014) 57:2874-2883. DOI 10.1021/jm401487x · PubMed

Other PDB entries of the same protein (UniProt O95931 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SII 1.37 Å, Crystal Structure of CBX7 with compound UNC4976
5EPJ 1.6 Å, Crystal Structure of chromodomain of CBX7 in complex with inhibitor UNC3866
6V2R 1.6 Å, Crystal Structure of chromodomain of CBX7 mutant V13A in complex with inhibitor UNC3866
3GS2 1.7 Å, Ring1B C-terminal domain/Cbx7 Cbox Complex
9V9P 3.4 Å, Cryo-EM structure of the cPRC1-di-nucleosome (CBX7) complex
2K1B Solution NMR structure of the chromo domain of the chromobox protein homolog 7
2L12 Solution NMR structure of the chromobox protein 7 with H3K9me3
2L1B Solution NMR structure of the chromobox protein Cbx7 with H3K27me3

Browse structure collections

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