3FDT: Chromobox protein homolog 5

Crystal structure of the complex of human chromobox homolog 5 (CBX5) with H3K9(me)3 peptide. Determined by X-ray diffraction at 2.0 Å resolution. Released 13 Jan 2009.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 529
Mol. weight: 8.81 kDa
Released: 13 Jan 2009

Explore 3FDT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FDT 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	3-5	3	1
β-strand	6-15	10	2
β-strand	18-25	8	2
α-helix	30-32	3
β-strand	34-37	4	2
α-helix	38-40	3
β-strand	41-42	2	1
α-helix	44-51	8

Chain T: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	15-17	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromobox protein homolog 5	A	protein	59	Homo sapiens	P45973 (AlphaFold model)
H3K9(me)3 peptide	T	protein	15	synthetic construct	P68431 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3FDT_1 Chromobox protein homolog 5 (chains A)
GEEYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEFMKKYKKMKE

Sequence of entity 2 (T), FASTA

>3FDT_2 H3K9(me)3 peptide (chains T)
ARTKQTARKSTGGKA

Primary citation

Recognition and specificity determinants of the human cbx chromodomains. Kaustov, L., Ouyang, H., Amaya, M. et al. J Biol Chem (2011) 286:521-529. DOI 10.1074/jbc.M110.191411 · PubMed

Other PDB entries of the same protein (UniProt P45973 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CEA 2.15 Å, Crystal structure of HP1alpha chromoshadow domain
9CDW 2.4 Å, Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide
3I3C 2.48 Å, Crystal Structural of CBX5 Chromo Shadow Domain
9CMT 3.17 Å, The crystal structure of HP1alpha CSD-Agno complex
8UXQ 6.3 Å, Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome

Browse structure collections

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