Research workbench
Crystal structure of SIR2TM in complex with acetyl P53 peptide and dadme-NAD+
Analyse Crystal structure of SIR2TM in complex with acetyl P53 peptide and dadme-NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D4B
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase; Acetyl P53 peptide
- EC
- 3.5.1.-
- UniProt
- Q9WYW0
- Ligands
- DZD, ZN
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent deacetylase (EC 3.5.1.-) | protein | 233 | 42% helix, 21% strand | Q9WYW0 |
| D | Acetyl P53 peptide | protein | 9 | 0% helix, 33% strand | — |
Ligands and binding sites
- DZD · 5'-O-[(R)-{[(R)-{[(3R,4R)-1-(3-carbamoylbenzyl)-4-hydroxypyrrolidin-3-yl]methoxy}(hydroxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine · ligand · chains A, D
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.67 | 0.84 | 34 | DZD |
Interfaces
1 interface between chains.
- A–D · 681 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 3D4B · Crystal structure of Sir2Tm in complex with Acetyl p53 peptide and DADMe-NAD+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WYW0 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase (Q9WYW0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9WYW0
- Elsewhere: RCSB PDB 3D4B · PDBe 3D4B · UniProt Q9WYW0
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