Research workbench
Crystal structure of SIRT3 in complex with acetyl P53 peptide coupled with 4-amino-7-methylcoumarin
Analyse Crystal structure of SIRT3 in complex with acetyl P53 peptide coupled with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FZ3
- Type
- protein
- Length
- 264 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-3, mitochondrial; Peptide from cellular tumor…
- EC
- 3.5.1.-
- UniProt
- Q9NTG7, P04637
- Ligands
- ACE, MCM, ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 260 | 41% helix, 18% strand | Q9NTG7 |
| B | Peptide from cellular tumor antigen P53 | protein | 4 | 0% helix, 25% strand | P04637 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B
- MCM · 7-amino-4-methyl-chromen-2-one · 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
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 | 444 | 0.68 | 0.79 | 37 | empty |
| 2 | 95 | 0.43 | 0.78 | 20 | empty |
| 3 | 110 | 0.38 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 401 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, acetylation).
Compared structures
- 4FZ3 · Crystal structure of SIRT3 in complex with acetyl p53 peptide coupled with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NTG7 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-3… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9NTG7
- Every structure of UniProt P04637
- Elsewhere: RCSB PDB 4FZ3 · PDBe 4FZ3 · UniProt Q9NTG7 · UniProt P04637
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