6V2D: Chromodomain of CDYL2

Crystal Structure of chromodomain of CDYL2 in complex with inhibitor UNC3866. Determined by X-ray diffraction at 2.1 Å resolution. Released 25 Dec 2019.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, synthetic construct
Chains: 12
Atoms: 3,488
Mol. weight: 51.45 kDa
Released: 25 Dec 2019

Explore 6V2D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V2D contains 19 α-helices and 38 β-strands across 12 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, E, I and K: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	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	1	1
α-helix	49-56	8

Chains B, D, F, H, J and L: 0 helices, 1 β-strand

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

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	6-7	2	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	1	3
α-helix	49-56	8

Chain G: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	7
β-strand	6-7	2	8
β-strand	9-17	9	9
β-strand	23-29	7	9
α-helix	34-36	3
β-strand	38-41	4	9
α-helix	42-44	3
β-strand	45	1	8
α-helix	49-56	8
α-helix	58-63	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromodomain Y-like protein 2	A, C, E, G, I, K	protein	64	Homo sapiens	Q8N8U2 (AlphaFold model)
UNC3866	B, D, F, H, J, L	protein	6	synthetic construct

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>6V2D_1 Chromodomain Y-like protein 2 (chains A, C, E, G, I, K)
GASGDLYEVERIVDKRKNKKGKWEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNGLHM
SKDK

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>6V2D_2 UNC3866 (chains B, D, F, H, J, L)
XFALXX

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
6V2H 2.6 Å, Crystal structure of CDYL2 in complex with H3tK27me3
6V3N 2.7 Å, Crystal structure of CDYL2 in complex with H3K27me3
6V8W 2.8 Å, CDYL2 chromodomain in complex with a synthetic peptide
2MJ8 Solution structure of CDYL2 chromodomain

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