HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4. Determined by X-ray diffraction at 3.3 Å resolution. Released 11 May 2016.
Explore 5ICN in 3D Show helices and sheets RCSB PDB PDBe
5ICN contains 27 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 | 175-182 | 8 | |
| α-helix | 191-193 | 3 | |
| β-strand | 195-199 | 5 | 1 |
| α-helix | 207-226 | 20 | |
| α-helix | 238-245 | 8 | |
| α-helix | 248-260 | 13 | |
| α-helix | 265-272 | 8 | |
| α-helix | 284-287 | 4 | |
| α-helix | 290-303 | 14 | |
| α-helix | 307-313 | 7 | |
| α-helix | 320-330 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 11-14 | 4 | 1 |
| α-helix | 17-20 | 4 | |
| α-helix | 33-44 | 12 | |
| α-helix | 48-50 | 3 | |
| β-strand | 52-56 | 5 | 1 |
| α-helix | 57-60 | 4 | |
| α-helix | 61-64 | 4 | |
| α-helix | 70-78 | 9 | |
| α-helix | 84-93 | 10 | |
| α-helix | 106-125 | 20 | |
| β-strand | 131-134 | 4 | 1 |
| β-strand | 143 | 1 | 2 |
| β-strand | 146 | 1 | 2 |
| β-strand | 148 | 1 | 3 |
| β-strand | 151 | 1 | 3 |
| α-helix | 155-163 | 9 | |
| β-strand | 170-174 | 5 | 1 |
| α-helix | 181-186 | 6 | |
| β-strand | 193-200 | 8 | 1 |
| α-helix | 217-219 | 3 | |
| β-strand | 223-228 | 6 | 1 |
| α-helix | 234-252 | 19 | |
| β-strand | 256-260 | 5 | 1 |
| β-strand | 266 | 1 | 4 |
| β-strand | 276 | 1 | 4 |
| α-helix | 278-290 | 13 | |
| β-strand | 295-298 | 4 | 1 |
| α-helix | 305-319 | 15 | |
| β-strand | 327 | 1 | 5 |
| α-helix | 328-330 | 3 | |
| α-helix | 334-336 | 3 | |
| β-strand | 342 | 1 | 5 |
| α-helix | 356-371 | 16 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Metastasis-associated protein MTA1 | A | protein | 195 | Homo sapiens | Q13330 (AlphaFold model) |
| Histone deacetylase 1 | B | protein | 376 | Homo sapiens | Q13547 (AlphaFold model) |
| Gly-ala-6A0-arg-his | C | protein | 9 | synthetic construct |
>5ICN_1 Metastasis-associated protein MTA1 (chains A) GAADKGEIRVGNRYQADITDLLKEGEEDGRDQSRLETQVWEAHNPLTDKQIDQFLVVARS VGTFARALDCSSSVRQPSLHMSAAAASRDITLFHAMDTLHKNIYDISKAISALVPQGGPV LCRDEMEEWSASEANLFEEALEKYGKDFTDIQQDFLPWKSLTSIIEYYYMWKTTDRYVQQ KRLKAAEAESKLKQV
>5ICN_2 Histone deacetylase 1 (chains B) MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKAN AEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAS AVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHG DGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAI FKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGG GGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLE KIKQRLFENLRMLPHA
>5ICN_3 GLY-ALA-6A0-ARG-HIS (chains C) LGKGGAXRH
Water and common crystallization additives (K) are not listed.
Insights into the activation mechanism of class I HDAC complexes by inositol phosphates. Watson, P.J., Millard, C.J., Riley, A.M. et al. Nat Commun (2016) 7:11262-11262. DOI 10.1038/ncomms11262 · PubMed
Other PDB entries of the same protein (UniProt Q13330 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 5ICN 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.