Research workbench
Complex of human SIRT3 with bromo-resveratrol and fluor-de-lys peptide
Analyse Complex of human SIRT3 with bromo-resveratrol and fluor-de-lys peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C7B
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-3, mitochondrial; Peptide
- EC
- 3.5.1.-
- UniProt
- Q9NTG7
- Ligands
- BVB, ZN
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 261 | 42% helix, 18% strand | Q9NTG7 |
| B | Peptide | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- BVB · 5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol · ligand · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 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 | 484 | 0.71 | 0.80 | 46 | BVB |
| 2 | 106 | 0.36 | 0.74 | 24 | GOL |
Interfaces
1 interface between chains.
- A–B · 440 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4C7B · Complex of human Sirt3 with Bromo-Resveratrol and Fluor-De-Lys peptide · 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
- Elsewhere: RCSB PDB 4C7B · PDBe 4C7B · UniProt Q9NTG7
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