2VQW: Inhibitor-free HDAC4 catalytic domain

Structure of inhibitor-free HDAC4 catalytic domain (with gain-of- function mutation His332Tyr). Determined by X-ray diffraction at 3.0 Å resolution. Released 5 Aug 2008.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 2,872
Mol. weight: 44.71 kDa
Ligands: ZN
Released: 5 Aug 2008

Explore 2VQW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VQW contains 22 α-helices and 15 β-strands across 1 chain. 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 G: 22 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	1
α-helix	16-20	5
α-helix	36-48	13
β-strand	55-57	3	1
α-helix	61-63	3
α-helix	64-67	4
α-helix	73-80	8
β-strand	103-104	2	2
β-strand	110-111	2	2
β-strand	117	1	2
α-helix	123-143	21
β-strand	148-151	4	1
β-strand	166	1	3
β-strand	169	1	3
α-helix	173-183	11
β-strand	190-194	5	1
α-helix	201-207	7
β-strand	213-220	8	1
α-helix	222-224	3
α-helix	239-241	3
β-strand	245-250	6	1
α-helix	257-258	2
α-helix	260-266	7
α-helix	267-271	5
α-helix	272-278	7
β-strand	282-287	6	1
β-strand	292	1	4
β-strand	304	1	4
α-helix	306-317	12
β-strand	324-328	5	1
α-helix	334-349	16
α-helix	353-356	4
α-helix	358-362	5
α-helix	363-366	4
α-helix	367-380	14
α-helix	391-392	2
α-helix	398-405	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 4	G	protein	413	HOMO SAPIENS	P56524 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>2VQW_1 HISTONE DEACETYLASE 4 (chains G)
GAMTKPRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGR
KATLEELQTVHSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNE
VHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKL
LQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGP
GVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLG
GYNLSARCFGYLTKQLMGLAGGRIVLALEGGYDLTAICDASEACVSALLGNELDPLPEKV
LQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEAETVT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

Primary citation

Structural and Functional Analysis of the Human Hdac4 Catalytic Domain Reveals a Regulatory Structural Zinc-Binding Domain. Bottomley, M.J., Lo Surdo, P., Di Giovine, P. et al. J Biol Chem (2008) 283:26694. DOI 10.1074/JBC.M803514200 · 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…

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