Research workbench
Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with saha
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
- 3C0Z
- 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
- SHH, 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 | 383 | 42% helix, 14% strand | Q8WUI4 |
| B | Histone deacetylase 7A | protein | 368 | 38% helix, 14% strand | Q8WUI4 |
| C | Histone deacetylase 7A | protein | 359 | 42% helix, 14% strand | Q8WUI4 |
Ligands and binding sites
- SHH · Octanedioic acid hydroxyamide phenylamide · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.61 | 0.74 | 66 | empty |
| 2 | 143 | 0.59 | 0.84 | 21 | SHH |
| 3 | 134 | 0.58 | 0.84 | 24 | SHH |
| 4 | 119 | 0.58 | 0.84 | 21 | SHH |
| 5 | 222 | 0.46 | 0.74 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 483 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 434 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3C0Z · 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 3C0Z · PDBe 3C0Z · UniProt Q8WUI4
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