Research workbench
Structural basis for nicotinamide inhibition and base exchange in SIR2 enzymes
Analyse Structural basis for nicotinamide inhibition and base exchange in SIR2 enzymes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OD9
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase HST2; H4 peptide
- EC
- 3.5.1.-
- UniProt
- P53686
- Ligands
- A1R, NCA, ZN
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent deacetylase HST2 (EC 3.5.1.-) | protein | 291 | 42% helix, 16% strand | P53686 |
| B | H4 peptide | protein | 7 | 0% helix, 29% 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
- NCA · Nicotinamide · 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 | 350 | 0.73 | 0.85 | 45 | A1R, NCA |
| 2 | 81 | 0.32 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 622 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 2OD9 · Structural Basis for Nicotinamide Inhibition and Base Exchange in Sir2 Enzymes · 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 2OD9 · PDBe 2OD9 · UniProt P53686
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