Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP1 fragment. Determined by X-ray diffraction at 1.85 Å resolution. Released 14 Nov 2018.
Explore 5ZOO in 3D Show helices and sheets RCSB PDB PDBe
5ZOO contains 26 α-helices and 21 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 |
|---|---|---|---|
| β-strand | 1360-1362 | 3 | 7 |
| β-strand | 1367-1370 | 4 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 654-657 | 4 | 1 |
| α-helix | 660-664 | 5 | |
| α-helix | 672-674 | 3 | |
| α-helix | 680-691 | 12 | |
| α-helix | 694-697 | 4 | |
| β-strand | 699-701 | 3 | 1 |
| α-helix | 705-707 | 3 | |
| α-helix | 708-711 | 4 | |
| α-helix | 717-724 | 8 | |
| β-strand | 747-748 | 2 | 2 |
| β-strand | 754-755 | 2 | 2 |
| β-strand | 761 | 1 | 2 |
| α-helix | 767-786 | 20 | |
| β-strand | 792-795 | 4 | 1 |
| β-strand | 805 | 1 | 3 |
| β-strand | 808 | 1 | 3 |
| β-strand | 810 | 1 | 4 |
| β-strand | 813 | 1 | 4 |
| α-helix | 817-829 | 13 | |
| β-strand | 834-838 | 5 | 1 |
| α-helix | 845-851 | 7 | |
| β-strand | 857-864 | 8 | 1 |
| α-helix | 866-868 | 3 | |
| α-helix | 883-885 | 3 | |
| β-strand | 889-894 | 6 | 1 |
| α-helix | 901-902 | 2 | |
| β-strand | 903 | 1 | 5 |
| α-helix | 904-910 | 7 | |
| α-helix | 911-915 | 5 | |
| α-helix | 916-922 | 7 | |
| β-strand | 926-931 | 6 | 1 |
| β-strand | 936 | 1 | 6 |
| α-helix | 941-943 | 3 | |
| β-strand | 947 | 1 | 5 |
| β-strand | 948 | 1 | 6 |
| α-helix | 950-960 | 11 | |
| α-helix | 964-966 | 3 | |
| β-strand | 968-972 | 5 | 1 |
| α-helix | 978-992 | 15 | |
| α-helix | 995-1001 | 7 | |
| α-helix | 1002-1006 | 5 | |
| α-helix | 1007-1010 | 4 | |
| α-helix | 1011-1024 | 14 | |
| α-helix | 1029-1031 | 3 | |
| α-helix | 1042-1052 | 11 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Histone deacetylase 4 | G | protein | 403 | Homo sapiens | P56524 (AlphaFold model) |
| SMRT corepressor SP1 fragment | A | protein | 14 | Homo sapiens | Q9Y618 (AlphaFold model) |
>5ZOO_1 Histone deacetylase 4 (chains G) AFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEE LQTVHSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGA ARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLS VSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNV NMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSA RCFGYLTKQLMGLAGGRIVLALEGGYDLTAICDASEACVSALLGNELDPLPEKVLQQRPN ANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEA
>5ZOO_2 SMRT corepressor SP1 fragment (chains A) HIRGSITQGIPRSY
| ID | Name | Formula | Copies |
|---|---|---|---|
| ZN | Zinc ion | Zn | 2 |
Water and common crystallization additives (K) are not listed.
Structural basis of the specific interaction of SMRT corepressor with histone deacetylase 4. Park, S.Y., Kim, G.S., Hwang, H.J. et al. Nucleic Acids Res (2018) 46:11776-11788. DOI 10.1093/nar/gky926 · PubMed
Other PDB entries of the same protein (UniProt P56524 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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