Research workbench
Structure of the yeast HST2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide
Analyse Structure of the yeast HST2 protein deacetylase in ternary complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q17
- Type
- protein
- Length
- 879 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HST2 protein
- UniProt
- P53686
- Ligands
- APR, ZN, CL
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HST2 protein | protein | 290 | 40% helix, 17% strand | P53686 |
| B | HST2 protein | protein | 294 | 42% helix, 17% strand | P53686 |
| C | HST2 protein | protein | 295 | 38% helix, 16% strand | P53686 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 4 copies · chains C, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.79 | 0.87 | 56 | APR |
| 2 | 428 | 0.79 | 0.87 | 54 | APR |
| 3 | 417 | 0.78 | 0.87 | 57 | APR |
| 4 | 1136 | 0.73 | 0.77 | 110 | empty |
| 5 | 384 | 0.67 | 0.80 | 50 | empty |
Interfaces
3 interfaces between chains.
- A–B · 892 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 767 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 762 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1Q17 · Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP… · the same entry in another collection · chain A against A, TM-score 1.00
- P53686 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase HST2 (P53686) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P53686
- Elsewhere: RCSB PDB 1Q17 · PDBe 1Q17 · UniProt P53686
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