Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10. Determined by X-ray diffraction at 1.95 Å resolution. Released 7 Aug 2024.
Explore 9CBT in 3D Show helices and sheets RCSB PDB PDBe
9CBT contains 40 α-helices and 26 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 | 164-166 | 3 | |
| α-helix | 176-180 | 5 | |
| β-strand | 181 | 1 | 2 |
| α-helix | 182-187 | 6 | |
| α-helix | 190-199 | 10 | |
| 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 | 3 |
| β-strand | 262-264 | 3 | 3 |
| α-helix | 265-268 | 4 | |
| α-helix | 269-273 | 5 | |
| β-strand | 279 | 1 | 4 |
| α-helix | 285 | 1 | |
| β-strand | 286 | 1 | 4 |
| β-strand | 287-291 | 5 | 3 |
| β-strand | 294 | 1 | 2 |
| α-helix | 297-299 | 3 | |
| α-helix | 300-304 | 5 | |
| α-helix | 305-311 | 7 | |
| β-strand | 314-318 | 5 | 1 |
| α-helix | 328-332 | 5 | |
| β-strand | 340-344 | 5 | 1 |
| α-helix | 350-353 | 4 | |
| β-strand | 359-363 | 5 | 1 |
| α-helix | 366-377 | 12 | |
| α-helix | 380-390 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 125-133 | 9 | |
| β-strand | 140-144 | 5 | 5 |
| α-helix | 146-148 | 3 | |
| α-helix | 150-152 | 3 | |
| α-helix | 164-166 | 3 | |
| α-helix | 176-180 | 5 | |
| β-strand | 181 | 1 | 6 |
| α-helix | 182-187 | 6 | |
| α-helix | 190-198 | 9 | |
| α-helix | 208-218 | 11 | |
| β-strand | 222-227 | 6 | 5 |
| α-helix | 233-236 | 4 | |
| α-helix | 241-243 | 3 | |
| β-strand | 244-246 | 3 | 5 |
| β-strand | 249-256 | 8 | 7 |
| β-strand | 262-264 | 3 | 7 |
| α-helix | 265-267 | 3 | |
| α-helix | 269-273 | 5 | |
| β-strand | 279 | 1 | 8 |
| α-helix | 285 | 1 | |
| β-strand | 286 | 1 | 8 |
| β-strand | 287-291 | 5 | 7 |
| β-strand | 294 | 1 | 6 |
| α-helix | 297-299 | 3 | |
| α-helix | 300-304 | 5 | |
| α-helix | 305-311 | 7 | |
| β-strand | 314-318 | 5 | 5 |
| α-helix | 328-332 | 5 | |
| β-strand | 340-344 | 5 | 5 |
| α-helix | 349-353 | 5 | |
| β-strand | 359-363 | 5 | 5 |
| α-helix | 366-377 | 12 | |
| α-helix | 380-394 | 15 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| NAD-dependent protein deacetylase sirtuin-3, mitochondrial | A, B | protein | 282 | Homo sapiens | Q9NTG7 (AlphaFold model) |
>9CBT_1 NAD-dependent protein deacetylase sirtuin-3, mitochondrial (chains A, B) SDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPE AIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVS GIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEP LPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRS RDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK
| ID | Name | Formula | Copies |
|---|---|---|---|
| 5I7 | (phenylmethyl) ~{N}-[(2~{S})-6-[[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[… | C51 H86 N9 O16 P2 S | 1 |
| 5IA | 2-{[(2S)-6-[(Z)-(1-{[(2R,3R,4R,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H… | C51 H86 N9 O16 P2 S | 1 |
| ZN | Zinc ion | Zn | 2 |
Water and common crystallization additives (PG4) are not listed.
A Mitochondria-Targeting SIRT3 Inhibitor with Activity against Diffuse Large B Cell Lymphoma. Jana, S., Shang, J., Hong, J.Y. et al. J Med Chem (2024) 67:15428-15437. DOI 10.1021/acs.jmedchem.4c01053 · PubMed
Other PDB entries of the same protein (UniProt Q9NTG7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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