MolNFT v1 · #141485 · protein
Crystal structure of SIRT3 in complex with H3K9BHB peptide
5Z93 · NAD-dependent protein deacetylase sirtuin-3, mitochondrial: “Crystal structure of SIRT3 in complex with H3K9BHB peptide”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.67). MolNFT v1 #141485 on GenesisL1: 3D…
- PDB
- 5Z93
- Type
- protein
- Length
- 281 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-3, mitochondrial; Gene for histone H3 (germline…
- EC
- 3.5.1.-
- UniProt
- Q9NTG7, V9H1G0
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 274 | 43% helix, 19% strand | Q9NTG7 |
| B | Gene for histone H3 (germline gene) | protein | 7 | 0% helix, 43% strand | V9H1G0 |
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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.67 | 0.86 | 34 | empty |
| 2 | 105 | 0.62 | 0.87 | 24 | empty |
| 3 | 90 | 0.35 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 540 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 5Z93 · Crystal Structure of SIRT3 in complex with H3K9bhb 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 0.94
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 V9H1G0
- Elsewhere: RCSB PDB 5Z93 · PDBe 5Z93 · UniProt Q9NTG7 · UniProt V9H1G0
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