Research workbench
Crystal structure of catalytic domain of human histone deacetylase HDAC7
Analyse Crystal structure of catalytic domain of human histone deacetylase HDAC7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C0Y
- Type
- protein
- Length
- 1,111 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 7A
- UniProt
- Q8WUI4
- Ligands
- ZN, K
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 7A | protein | 386 | 42% helix, 14% strand | Q8WUI4 |
| B | Histone deacetylase 7A | protein | 367 | 38% helix, 15% strand | Q8WUI4 |
| C | Histone deacetylase 7A | protein | 358 | 39% helix, 15% strand | Q8WUI4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- K · Potassium ion · metal · 6 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.61 | 0.87 | 24 | empty |
| 2 | 132 | 0.61 | 0.85 | 25 | empty |
| 3 | 129 | 0.57 | 0.83 | 23 | empty |
| 4 | 222 | 0.56 | 0.78 | 23 | empty |
| 5 | 316 | 0.54 | 0.75 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–B · 489 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 389 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3C0Y · Crystal structure of catalytic domain of human histone deacetylase HDAC7 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WUI4 · AlphaFold monomer V2.0 prediction for histone deacetylase 7 (Q8WUI4) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q8WUI4
- Elsewhere: RCSB PDB 3C0Y · PDBe 3C0Y · UniProt Q8WUI4
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