Research workbench
Complex structure of CDYL2 with an antagonist
Analyse Complex structure of CDYL2 with an antagonist in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SLW
- Type
- protein
- Length
- 364 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromodomain Y-like protein 2
- UniProt
- Q8N8U2
- Ligands
- 5R0, UNX
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Chromodomain Y-like protein 2 | protein | 56 | 25% helix, 41% strand | Q8N8U2 |
| G, H, I, J, K, L | Chromodomain Y-like protein 2 | protein | 5 | 0% helix, 40% strand | — |
| B | Chromodomain Y-like protein 2 | protein | 55 | 20% helix, 42% strand | Q8N8U2 |
| C | Chromodomain Y-like protein 2 | protein | 54 | 20% helix, 43% strand | Q8N8U2 |
| F | Chromodomain Y-like protein 2 | protein | 57 | 25% helix, 42% strand | Q8N8U2 |
Ligands and binding sites
- 5R0 · 4-~{tert}-butylbenzoic acid · ligand · 6 copies · chains A, G, B, H, C, I, D, J, E, K, F, L
- UNX · Unknown atom or ion · ion · 3 copies · chains B, C, F, D, E
- GOL · Glycerol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.54 | 0.87 | 19 | empty |
| 2 | 67 | 0.40 | 0.80 | 16 | UNX |
| 3 | 94 | 0.38 | 0.76 | 18 | 5R0 |
| 4 | 99 | 0.37 | 0.75 | 22 | 5R0, UNX |
| 5 | 84 | 0.34 | 0.74 | 14 | 5R0 |
Interfaces
31 interfaces between chains.
- F–L · 604 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 598 Ų buried · 12 hydrogen bonds · protein-protein
- D–J · 593 Ų buried · 11 hydrogen bonds · protein-protein
- E–K · 587 Ų buried · 11 hydrogen bonds · protein-protein
- A–G · 581 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 6 modified (covalent ligand, nonstandard).
Compared structures
- Q8N8U2 · AlphaFold monomer V2.0 prediction for chromodomain Y-like protein 2 (Q8N8U2) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 7SLW · PDBe 7SLW · UniProt Q8N8U2
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