MolNFT v2 · #122614 · protein
Structure of the histone deacetylase Clr3
5IKK: “Structure of the histone deacetylase Clr3”. X-ray diffraction at 2.4, 5 ligands (ZN, K, MG), 4 pockets (best druggability 0.66). MolNFT v2 #122614 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IKK
- Type
- protein
- Length
- 594 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Schizosaccharomyces pombe 972h-
- Molecule
- Histone deacetylase clr3
- EC
- 3.5.1.98
- UniProt
- P56523
- Ligands
- ZN, K, MG, NO3, SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase clr3 (EC 3.5.1.98) | protein | 594 | 39% helix, 16% strand | P56523 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
- K · Potassium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- NO3 · Nitrate ion · ion · 3 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.66 | 0.79 | 50 | empty |
| 2 | 133 | 0.53 | 0.81 | 25 | empty |
| 3 | 59 | 0.48 | 0.85 | 16 | EDO |
| 4 | 58 | 0.26 | 0.73 | 11 | empty |
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 P56523
- Elsewhere: RCSB PDB 5IKK · PDBe 5IKK · UniProt P56523
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