MolNFT v1 · #46725 · protein
Crystal structure of YHST2 bound to the intermediate analogue ADP-hpd, and and aceylated H4 peptide
2OD7 · NAD-dependent deacetylase HST2: “Crystal structure of YHST2 bound to the intermediate analogue ADP-hpd, and and aceylated H4 peptide”. X-ray diffraction, 2 ligands (A1R, ZN), 2 pockets (best druggability 0.72). MolNFT v1 #46725 on…
- PDB
- 2OD7
- Type
- protein
- Length
- 297 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase HST2; Acetylated histone H4 peptide
- EC
- 3.5.1.-
- UniProt
- P53686
- Ligands
- A1R, ZN
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent deacetylase HST2 (EC 3.5.1.-) | protein | 289 | 42% helix, 17% strand | P53686 |
| B | Acetylated histone H4 peptide | protein | 8 | 0% helix, 38% strand | — |
Ligands and binding sites
- A1R · 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-dihydroxypyrrolidin-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy) phosphoryl]adenosine · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.72 | 0.84 | 44 | A1R |
| 2 | 79 | 0.29 | 0.72 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 640 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 2OD7 · Crystal Structure of yHst2 bound to the intermediate analogue ADP-HPD, and and aceylated… · 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 0.93
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 2OD7 · PDBe 2OD7 · UniProt P53686
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