Research workbench
Crystal structure of CDYL2 in complex with H3TK27ME3
Analyse Crystal structure of CDYL2 in complex with H3TK27ME3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V2H
- Type
- protein
- Length
- 408 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromodomain Y-like protein 2; H3TK27ME3
- UniProt
- Q8N8U2
- Ligands
- ACE, NI, UNX
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromodomain Y-like protein 2 | protein | 57 | 25% helix, 44% strand | Q8N8U2 |
| B, D, F, J, L | H3TK27ME3 | protein | 9 | 0% helix, 44% strand | — |
| C, E | Chromodomain Y-like protein 2 | protein | 60 | 23% helix, 42% strand | Q8N8U2 |
| G, I | Chromodomain Y-like protein 2 | protein | 59 | 24% helix, 42% strand | Q8N8U2 |
| H | H3TK27ME3 | protein | 10 | 0% helix, 40% strand | — |
| K | Chromodomain Y-like protein 2 | protein | 58 | 24% helix, 43% strand | Q8N8U2 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 6 copies · chains A, B, E, F, C, D, G, H, I, J, K, L
- NI · Nickel (II) ion · metal · 6 copies · chains A, C, E, G, I, K
- UNX · Unknown atom or ion · ion · 29 copies · chains A, I, B, F, E, C, G, H, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.78 | 0.79 | 103 | UNX |
| 2 | 69 | 0.30 | 0.74 | 16 | UNX |
Interfaces
20 interfaces between chains.
- G–H · 762 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 752 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 751 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 750 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 734 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 6 modified (covalent ligand, methylation).
Compared structures
- 6V2H · Crystal structure of CDYL2 in complex with H3tK27me3 · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8N8U2
- Elsewhere: RCSB PDB 6V2H · PDBe 6V2H · UniProt Q8N8U2
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