Research workbench
Acetyltransferase domain of CDY1
Analyse Acetyltransferase domain of CDY1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FBM
- Type
- protein
- Length
- 751 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Y chromosome chromodomain protein 1, telomeric isoform B
- UniProt
- Q9Y6F8
- Ligands
- CL
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Y chromosome chromodomain protein 1, telomeric isoform B | protein | 251 | 52% helix, 16% strand | Q9Y6F8 |
| B, C | Y chromosome chromodomain protein 1, telomeric isoform B | protein | 250 | 54% helix, 16% strand | Q9Y6F8 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.83 | 0.89 | 71 | empty |
| 2 | 104 | 0.42 | 0.77 | 16 | empty |
| 3 | 94 | 0.39 | 0.76 | 16 | empty |
| 4 | 77 | 0.39 | 0.78 | 15 | empty |
| 5 | 84 | 0.37 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1234 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1195 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1164 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 Q9Y6F8
- Elsewhere: RCSB PDB 2FBM · PDBe 2FBM · UniProt Q9Y6F8
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