Research workbench
Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent SIR2 HISTONE/PROTEIN deacetylases
Analyse Structural basis for nicotinamide cleavage and ADP-ribose transfer by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SZD
- Type
- protein
- Length
- 299 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase HST2; Histone H4 peptide
- EC
- 3.5.1.-
- UniProt
- P53686, P02309
- Ligands
- APR, ZN, CL
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent deacetylase HST2 (EC 3.5.1.-) | protein | 291 | 41% helix, 16% strand | P53686 |
| B | Histone H4 peptide | protein | 8 | 0% helix, 38% strand | P02309 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
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 | 322 | 0.72 | 0.85 | 45 | APR |
| 2 | 99 | 0.33 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 618 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 1SZD · Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2… · 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 0.94
- P02309 · AlphaFold monomer V2.0 prediction for histone H4 (P02309) · a predicted model of the same protein · chain B against A, TM-score 0.39
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 P02309
- Elsewhere: RCSB PDB 1SZD · PDBe 1SZD · UniProt P53686 · UniProt P02309
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