8SP6: Complex structure of CDYL2 with an antagonist

Complex structure of CDYL2 with an antagonist. Determined by X-ray diffraction at 1.45 Å resolution. Released 13 Mar 2024.

Method: X-ray diffraction
Resolution: 1.45 Å
Organisms: Homo sapiens, synthetic construct
Chains: 12
Atoms: 3,733
Mol. weight: 50.12 kDa
Ligands: I9A
Released: 13 Mar 2024

Explore 8SP6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SP6 contains 18 α-helices and 37 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.

Chain A: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
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, E and F: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
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 C: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	3
β-strand	6-7	2	5
β-strand	9-17	9	6
β-strand	23-29	7	6
β-strand	38-41	4	6
α-helix	42-44	3
β-strand	45	1	5
α-helix	49-56	8

Chains G, H, I, J, K and L: 0 helices, 1 β-strand

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromodomain Y-like protein 2	A, B, C, D, E, F	protein	62	Homo sapiens	Q8N8U2 (AlphaFold model)
(5R0)FAL(MLZ)(5R5)	G, H, I, J, K, L	protein	6	synthetic construct

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>8SP6_1 Chromodomain Y-like protein 2 (chains A, B, C, D, E, F)
GASGDLYEVERIVDKRKNKKGKWEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNGLHM
SK

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>8SP6_2 (5R0)FAL(MLZ)(5R5) (chains G, H, I, J, K, L)
XFALKX

Ligands and cofactors

ID	Name	Formula	Copies
I9A	(1s,4s)-bicyclo[2.2.1]heptane	C7 H12	6

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

Primary citation

COMPLEX STRUCTURE OF CDYL2 WITH AN ANTAGONIST. Song, X., Beldar, S., Dong, A. et al. To be published.

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

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
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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