Research workbench
Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with trichostatin a (tsa)
Analyse Crystal structure of catalytic domain of human histone deacetylase HDAC7 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C10
- Type
- protein
- Length
- 1,110 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 7A
- UniProt
- Q8WUI4
- Ligands
- TSN, ZN, K
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 7A | protein | 383 | 42% helix, 14% strand | Q8WUI4 |
| B | Histone deacetylase 7A | protein | 368 | 39% helix, 15% strand | Q8WUI4 |
| C | Histone deacetylase 7A | protein | 359 | 42% helix, 14% strand | Q8WUI4 |
Ligands and binding sites
- TSN · Trichostatin A · ligand · 3 copies · chains A, B, C
- 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 | 114 | 0.58 | 0.85 | 24 | ZN, TSN |
| 2 | 131 | 0.58 | 0.84 | 21 | TSN |
| 3 | 106 | 0.58 | 0.85 | 22 | TSN |
| 4 | 368 | 0.56 | 0.74 | 57 | empty |
| 5 | 324 | 0.54 | 0.75 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 488 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 408 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3C10 · Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with… · 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 3C10 · PDBe 3C10 · UniProt Q8WUI4
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