5ZOP: Histone deacetylase 4

Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP2 fragment. Determined by X-ray diffraction at 2.7 Å resolution. Released 10 Oct 2018.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,101
Mol. weight: 44.5 kDa
Ligands: ZN
Released: 10 Oct 2018

Explore 5ZOP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ZOP contains 25 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.

Chain A: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3

Chain G: 24 helices, 15 β-strands

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	810	1	3
β-strand	813	1	3
α-helix	817-829	13
β-strand	834-838	5	1
α-helix	845-850	6
β-strand	857-864	8	1
α-helix	883-885	3
β-strand	889-894	6	1
α-helix	901-902	2
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	4
α-helix	941-943	3
β-strand	948	1	4
α-helix	950-960	11
α-helix	963-966	4
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	1042-1048	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 4	G	protein	399	Homo sapiens	P56524 (AlphaFold model)
SMRT corepressor SP2 fragment	A	protein	12	Homo sapiens	Q9Y618 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>5ZOP_1 Histone deacetylase 4 (chains G)
FTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEEL
QTVHSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAA
RLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSV
SKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVN
MAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAR
CFGYLTKQLMGLAGGRIVLALEGGYDLTAICDASEACVSALLGNELDPLPEKVLQQRPNA
NAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCEN

Sequence of entity 2 (A), FASTA

>5ZOP_2 SMRT corepressor SP2 fragment (chains A)
EGSITQGTPLKY

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (K) are not listed.

Primary citation

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:

3V31 1.57 Å, Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human…
2VQM 1.8 Å, Structure of HDAC4 catalytic domain bound to a hydroxamic acid inhbitor
3UXG 1.85 Å, Crystal structure of RFXANK
5ZOO 1.85 Å, Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor…
3UZD 1.86 Å, Crystal structure of 14-3-3 GAMMA
2VQQ 1.9 Å, Structure of HDAC4 catalytic domain (a double cysteine-to-alanine mutant) bound to a…
2VQJ 2.1 Å, Structure of HDAC4 catalytic domain bound to a trifluoromethylketone inhbitor
2VQO 2.15 Å, Structure of HDAC4 catalytic domain with a gain-of-function muation bound to a…
6FYZ 2.15 Å, Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa…
8PDE 2.4 Å, Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC4…
2H8N 2.6 Å, Structure of a glutamine-rich domain from histone deacetylase 4
5A2S 2.65 Å, Potent, selective and CNS-penetrant tetrasubstituted cyclopropane class IIa histone…

Browse structure collections

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