Crystal structure of human SIRT3 in complex with native alkylimidate formed from acetyl-lysine ACS2-peptide crystallized in presence of the inhibitor ex-527. Determined by X-ray diffraction at 2.5 Å resolution. Released 17 Jul 2013.
Explore 4BVG in 3D Show helices and sheets RCSB PDB PDBe
4BVG contains 22 α-helices and 15 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 125-133 | 9 | |
| β-strand | 140-144 | 5 | 1 |
| α-helix | 146-148 | 3 | |
| α-helix | 150-152 | 3 | |
| α-helix | 176-180 | 5 | |
| α-helix | 182-187 | 6 | |
| α-helix | 190-198 | 9 | |
| α-helix | 208-218 | 11 | |
| β-strand | 222-227 | 6 | 1 |
| α-helix | 233-236 | 4 | |
| α-helix | 241-243 | 3 | |
| β-strand | 244-246 | 3 | 1 |
| β-strand | 249-256 | 8 | 2 |
| β-strand | 262-264 | 3 | 2 |
| α-helix | 265-268 | 4 | |
| α-helix | 269-273 | 5 | |
| α-helix | 276-278 | 3 | |
| β-strand | 279 | 1 | 3 |
| α-helix | 285 | 1 | |
| β-strand | 286 | 1 | 3 |
| β-strand | 287-291 | 5 | 2 |
| α-helix | 292-293 | 2 | |
| β-strand | 297 | 1 | 4 |
| α-helix | 298-299 | 2 | |
| α-helix | 300-304 | 5 | |
| α-helix | 305-311 | 7 | |
| β-strand | 314-318 | 5 | 1 |
| β-strand | 324-325 | 2 | 5 |
| α-helix | 328-333 | 6 | |
| β-strand | 340-344 | 5 | 1 |
| α-helix | 350-353 | 4 | |
| β-strand | 359-363 | 5 | 1 |
| α-helix | 366-376 | 11 | |
| α-helix | 380-387 | 8 | |
| α-helix | 388-392 | 5 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | -1 | 1 | 4 |
| β-strand | 1-2 | 2 | 5 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| NAD-dependent protein deacetylase sirtuin-3, mitochondrial | A | protein | 284 | HOMO SAPIENS | Q9NTG7 (AlphaFold model) |
| Acetyl-coenzyme a synthetase 2-like, mitochondrial | B | protein | 10 | HOMO SAPIENS | Q9NUB1 (AlphaFold model) |
>4BVG_1 NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL (chains A) GSSDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPY PEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLER VSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFG EPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHP RSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK
>4BVG_2 ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL (chains B) TRSGKVMRRL
| ID | Name | Formula | Copies |
|---|---|---|---|
| ZN | Zinc ion | Zn | 1 |
| XYQ | (2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihy… | C17 H25 N5 O15 P2 | 1 |
Water and common crystallization additives (EDO, GOL, SO4, PEG) are not listed.
Ex-527 inhibits Sirtuins by exploiting their unique NAD+-dependent deacetylation mechanism. Gertz, M., Fischer, F., Nguyen, G.T. et al. Proc Natl Acad Sci U S A (2013) 110:E2772-E2781. DOI 10.1073/pnas.1303628110 · PubMed
Other PDB entries of the same protein (UniProt Q9NTG7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 4BVG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.