6V3N: CDYL2

Crystal structure of CDYL2 in complex with H3K27me3. Determined by X-ray diffraction at 2.7 Å resolution. Released 1 Apr 2020.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,207
Mol. weight: 18.68 kDa
Released: 1 Apr 2020

Explore 6V3N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V3N contains 8 α-helices and 12 β-strands across 4 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: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	1
β-strand	9-17	9	2
β-strand	23-29	7	2
α-helix	34-36	3
β-strand	38-41	4	2
α-helix	42-44	3
β-strand	45-48	4	1

Chain B: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	3
β-strand	9-17	9	4
β-strand	23-29	7	4
α-helix	34-36	3
β-strand	38-41	4	4
α-helix	42-44	3
β-strand	45-48	4	3
α-helix	54-60	7

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	21	1
β-strand	22-27	6	1
α-helix	28	1

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	22-26	5	3
α-helix	27-28	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromodomain Y-like protein 2	A, B	protein	64	Homo sapiens	Q8N8U2 (AlphaFold model)
Ace-gln-leu-ala-thr-lys-ala-ala-arg-M3L-ser-ala-pro-ala-thr-tyr-NH2	C, D	protein	17	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6V3N_1 Chromodomain Y-like protein 2 (chains A, B)
GASGDLYEVERIVDKRKNKKGKWEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNGLHM
SKDK

Sequence of entity 2 (C, D), FASTA

>6V3N_2 ACE-GLN-LEU-ALA-THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA-THR-TYR-NH2 (chains C, D)
XQLATKAARKSAPATYX

Primary citation

Structural Basis for the Binding Selectivity of Human CDY Chromodomains. Dong, C., Liu, Y., Lyu, T.J. et al. Cell Chem Biol (2020) 27:827-838.e7. DOI 10.1016/j.chembiol.2020.05.007 · PubMed

Other PDB entries of the same protein (UniProt Q8N8U2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SP6 1.45 Å, Complex structure of CDYL2 with an antagonist
4HAE 2.0 Å, Crystal structure of the CDYL2-chromodomain
5JJZ 2.0 Å, Chromo domain of human Chromodomain Protein, Y-Like 2
6V2D 2.1 Å, Crystal Structure of chromodomain of CDYL2 in complex with inhibitor UNC3866
6V2H 2.6 Å, Crystal structure of CDYL2 in complex with H3tK27me3
6V8W 2.8 Å, CDYL2 chromodomain in complex with a synthetic peptide
2MJ8 Solution structure of CDYL2 chromodomain

Browse structure collections

About this viewer

MolViewer shows 6V3N directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.