Crystal structure of Sir2Tm in complex with Acetyl p53 peptide and DADMe-NAD+. Determined by X-ray diffraction at 1.9 Å resolution. Released 30 Sept 2008.
Explore 3D4B in 3D Show helices and sheets RCSB PDB PDBe
3D4B contains 17 α-helices and 17 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 | 3-12 | 10 | |
| β-strand | 16-20 | 5 | 1 |
| α-helix | 22-24 | 3 | |
| α-helix | 26-28 | 3 | |
| β-strand | 49 | 1 | 2 |
| α-helix | 50-55 | 6 | |
| α-helix | 57-67 | 11 | |
| α-helix | 69-72 | 4 | |
| α-helix | 74-76 | 3 | |
| α-helix | 78-88 | 11 | |
| β-strand | 94-97 | 4 | 1 |
| α-helix | 103-106 | 4 | |
| β-strand | 112-114 | 3 | 1 |
| β-strand | 117-124 | 8 | 3 |
| β-strand | 130-132 | 3 | 3 |
| α-helix | 133-139 | 7 | |
| β-strand | 147 | 1 | 4 |
| α-helix | 153 | 1 | |
| β-strand | 154 | 1 | 4 |
| β-strand | 155-159 | 5 | 3 |
| β-strand | 162 | 1 | 2 |
| β-strand | 165 | 1 | 5 |
| α-helix | 166-167 | 2 | |
| α-helix | 168-180 | 13 | |
| β-strand | 183-187 | 5 | 1 |
| β-strand | 193-194 | 2 | 6 |
| α-helix | 196-198 | 3 | |
| α-helix | 199-205 | 7 | |
| β-strand | 209-213 | 5 | 1 |
| α-helix | 221-223 | 3 | |
| β-strand | 226-228 | 3 | 1 |
| α-helix | 232-243 | 12 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 10 | 1 | 5 |
| β-strand | 12-13 | 2 | 6 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| NAD-dependent deacetylase | A | protein | 246 | Thermotoga maritima | Q9WYW0 (AlphaFold model) |
| Acetyl P53 peptide | D | protein | 9 |
>3D4B_1 NAD-dependent deacetylase (chains A) MKMKEFLDLLNESRLTVTLTGAGISTPSGIPDFRGPNGIYKKYSQNVFDIDFFYSHPEEF YRFAKEGIFPMLQAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQRAGSKKVIELHGNVE EYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLIRPNIVFFGENLPQDALREAIGLSSR ASLMIVLGSSLVVYPAAELPLITVRSGGKLVIVNLGETPFDDIATLKYNMDVVEFARRVM EEGGIS
>3D4B_2 Acetyl P53 peptide (chains D) TSRHKKLMA
| ID | Name | Formula | Copies |
|---|---|---|---|
| DZD | 5'-O-[(R)-{[(R)-{[(3R,4R)-1-(3-carbamoylbenzyl)-4-hydroxypyrrolidin-3-yl]methox… | C24 H33 N7 O11 P2 | 1 |
| ZN | Zinc ion | Zn | 1 |
Structural insights into intermediate steps in the Sir2 deacetylation reaction. Hawse, W.F., Hoff, K.G., Fatkins, D.G. et al. Structure (2008) 16:1368-1377. DOI 10.1016/j.str.2008.05.015 · PubMed
Other PDB entries of the same protein (UniProt Q9WYW0 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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