MolNFT v1 · #178094 · protein
Crystal structure of HST2 in complex with H3K9BZ peptide
7F4E · NAD-dependent protein deacetylase HST2: “Crystal structure of HST2 in complex with H3K9BZ peptide”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.67). MolNFT v1 #178094 on GenesisL1: 3D structure, binding sites…
- PDB
- 7F4E
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase HST2; Histone H3
- EC
- 2.3.1.286
- UniProt
- P53686, P61830
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase HST2 (EC 2.3.1.286) | protein | 278 | 41% helix, 17% strand | P53686 |
| C | Histone H3 | protein | 9 | 0% helix, 22% strand | P61830 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.67 | 0.87 | 34 | empty |
| 2 | 97 | 0.35 | 0.74 | 22 | empty |
| 3 | 53 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 648 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 7F4E · Crystal structure of Hst2 in complex with H3K9bz peptide · 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
- P61830 · AlphaFold monomer V2.0 prediction for histone H3 (P61830) · a predicted model of the same protein · chain C against A, TM-score 0.24
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
- Every structure of UniProt P61830
- Elsewhere: RCSB PDB 7F4E · PDBe 7F4E · UniProt P53686 · UniProt P61830
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