Research workbench
Crystal structure of SIRT3 with a H3K9 peptide containing a myristoyl lysine
Analyse Crystal structure of SIRT3 with a H3K9 peptide containing a myristoyl lysine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BWN
- Type
- protein
- Length
- 283 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myristoyl H3K9 peptide; NAD-dependent protein deacetylase sirtuin-3, mitochondrial
- EC
- 3.5.1.-
- UniProt
- Q9NTG7
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Myristoyl H3K9 peptide | protein | 9 | 0% helix, 22% strand | — |
| A | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 274 | 42% helix, 18% strand | Q9NTG7 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.59 | 0.85 | 17 | empty |
| 2 | 120 | 0.45 | 0.78 | 23 | empty |
| 3 | 112 | 0.37 | 0.74 | 26 | empty |
| 4 | 63 | 0.32 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 781 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 5BWN · Crystal Structure of SIRT3 with a H3K9 Peptide Containing a Myristoyl Lysine · the same entry in another collection · chain B against B, 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 5BWN · PDBe 5BWN · UniProt Q9NTG7
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