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Crystal structure of HDA15 hd domain
Analyse Crystal structure of HDA15 hd domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J6T
- Type
- protein
- Length
- 1,404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 15
- EC
- 3.5.1.98
- UniProt
- Q8GXJ1
- Ligands
- ZN, K, SO4
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 15 (EC 3.5.1.98) | protein | 353 | 42% helix, 15% strand | Q8GXJ1 |
| B | Histone deacetylase 15 (EC 3.5.1.98) | protein | 356 | 42% helix, 16% strand | Q8GXJ1 |
| C | Histone deacetylase 15 (EC 3.5.1.98) | protein | 344 | 42% helix, 15% strand | Q8GXJ1 |
| D | Histone deacetylase 15 (EC 3.5.1.98) | protein | 351 | 42% helix, 16% strand | Q8GXJ1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.80 | 0.84 | 76 | empty |
| 2 | 850 | 0.77 | 0.81 | 90 | SO4 |
| 3 | 164 | 0.45 | 0.75 | 24 | empty |
| 4 | 140 | 0.42 | 0.75 | 24 | empty |
| 5 | 149 | 0.41 | 0.74 | 19 | empty |
Interfaces
6 interfaces between chains.
- B–C · 630 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 628 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 625 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 335 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 298 Ų buried · 3 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 Q8GXJ1
- Elsewhere: RCSB PDB 6J6T · PDBe 6J6T · UniProt Q8GXJ1
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