MolNFT v1 · #65054 · protein
Crystal structure of human SIRT3 with acetyl-lysine ACECS2 peptide
3GLR · NAD-dependent deacetylase sirtuin-3, mitochondrial: “Crystal structure of human SIRT3 with acetyl-lysine ACECS2 peptide”. X-ray diffraction, 3 ligands (BCT, ZN, SO4), 3 pockets (best druggability 0.72). MolNFT v1 #65054 on…
- PDB
- 3GLR
- Type
- protein
- Length
- 281 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase sirtuin-3, mitochondrial; Acetyl-coenzyme a synthetase 2-like…
- EC
- 3.5.1.-, 6.2.1.1
- UniProt
- Q9NTG7, Q9NUB1
- Ligands
- BCT, ZN, SO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 274 | 43% helix, 18% strand | Q9NTG7 |
| B | Acetyl-coenzyme a synthetase 2-like, mitochondrial (EC 6.2.1.1) | protein | 7 | 0% helix, 43% strand | Q9NUB1 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 343 | 0.72 | 0.84 | 36 | empty |
| 2 | 51 | 0.33 | 0.78 | 10 | empty |
| 3 | 77 | 0.31 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 597 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 3GLR · Crystal Structure of human SIRT3 with acetyl-lysine AceCS2 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 0.96
- Q9NUB1 · AlphaFold monomer V2.0 prediction for acetyl-coenzyme a synthetase 2-like, mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.50
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 Q9NUB1
- Elsewhere: RCSB PDB 3GLR · PDBe 3GLR · UniProt Q9NTG7 · UniProt Q9NUB1
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