6V8W: CDYL2 chromodomain
CDYL2 chromodomain in complex with a synthetic peptide. Determined by X-ray diffraction at 2.8 Å resolution. Released 15 Jan 2020.
- Method
- X-ray diffraction
- Resolution
- 2.8 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 52
- Atoms
- 12,251
- Mol. weight
- 213.26 kDa
- Released
- 15 Jan 2020
Explore 6V8W in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6V8W contains 52 α-helices and 220 β-strands across 52 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, B, G, K, O, P, Q, T, V, X and Y: 2 helices, 7 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 |
| β-strand | 46-50 | 5 | 3 |
| β-strand | 52 | 1 | 4 |
Chains AA, BB, GG, KK, OO, PP, QQ, TT, UU, VV, XX and YY: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 1 |
Chains C, D, E, F, I, J, L, M, N, R, S, W and Z: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6 | 1 | 13 |
| β-strand | 7 | 1 | 14 |
| β-strand | 9-17 | 9 | 8 |
| β-strand | 23-29 | 7 | 8 |
| α-helix | 34-36 | 3 | |
| β-strand | 38-41 | 4 | 8 |
| α-helix | 42-44 | 3 | |
| β-strand | 45 | 1 | 14 |
| β-strand | 46-50 | 5 | 15 |
| β-strand | 52 | 1 | 16 |
Chains CC, DD, EE, FF, HH, II, JJ, LL, MM, NN, RR, SS, WW and ZZ: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 14 |
Chain H: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6 | 1 | 35 |
| β-strand | 7 | 1 | 39 |
| β-strand | 9-17 | 9 | 40 |
| β-strand | 23-29 | 7 | 40 |
| α-helix | 34-36 | 3 | |
| β-strand | 38-41 | 4 | 40 |
| α-helix | 42-44 | 3 | |
| β-strand | 45 | 1 | 39 |
| β-strand | 46-50 | 5 | 37 |
Chain U: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-7 | 2 | 41 |
| β-strand | 9-17 | 9 | 42 |
| β-strand | 23-29 | 7 | 42 |
| α-helix | 34-36 | 3 | |
| β-strand | 38-41 | 4 | 42 |
| α-helix | 42-44 | 3 | |
| β-strand | 45 | 1 | 41 |
| β-strand | 46-50 | 5 | 43 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Chromodomain Y-like protein 2 | A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z | protein | 62 | Homo sapiens | Q8N8U2 (AlphaFold model) |
| Iva-phe-ala-phe-5T3-ser-NH2 | AA, BB, CC, DD, EE, FF, GG, HH, II, JJ, KK, LL, MM, NN, OO, PP, QQ, RR, SS, TT, UU, VV, WW, XX, YY, ZZ | protein | 7 | synthetic construct | |
Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z), FASTA
>6V8W_1 Chromodomain Y-like protein 2 (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z)
GASGDLYEVERIVDKRKNKKGKWEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNGLHM
SK
Sequence of entity 2 (AA, BB, CC, DD, EE, FF, GG, HH, II, JJ, KK, LL, MM, NN, OO, PP, QQ, RR, SS, TT, UU, VV, WW, XX, YY, ZZ), FASTA
>6V8W_2 IVA-PHE-ALA-PHE-5T3-SER-NH2 (chains AA, BB, CC, DD, EE, FF, GG, HH, II, JJ, KK, LL, MM, NN, OO, PP, QQ, RR, SS, TT, UU, VV, WW, XX, YY, ZZ)
XFAFXSX
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
- 6V3N 2.7 Å, Crystal structure of CDYL2 in complex with H3K27me3
- 2MJ8 Solution structure of CDYL2 chromodomain
Browse structure collections
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