2VQV: Histone deacetylase 4

Structure of HDAC4 catalytic domain with a gain-of-function mutation bound to a hydroxamic acid inhibitor. Determined by X-ray diffraction at 3.3 Å resolution. Released 22 Jul 2008.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 5,406
Mol. weight: 90.28 kDa
Ligands: ZN, HA3
Released: 22 Jul 2008

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

Secondary structure: helices and β-sheets

2VQV contains 49 α-helices and 39 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: 25 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
β-strand	11-13	3	2
α-helix	16-18	3
α-helix	37-48	12
α-helix	50-53	4
β-strand	55-57	3	2
α-helix	58	1
α-helix	61-63	3
α-helix	64-67	4
α-helix	73-80	8
α-helix	117-142	26
β-strand	148	1	1
β-strand	149-151	3	2
β-strand	161	1	3
β-strand	164	1	3
β-strand	166	1	4
β-strand	169	1	4
α-helix	173-185	13
β-strand	190	1	5
β-strand	194	1	2
α-helix	201-206	6
β-strand	213	1	5
β-strand	215-220	6	2
α-helix	239-241	3
β-strand	245-250	6	2
β-strand	259	1	6
α-helix	260-266	7
α-helix	267-271	5
α-helix	272-278	7
β-strand	282	1	5
β-strand	283-287	5	2
β-strand	292	1	7
β-strand	303	1	6
β-strand	304	1	7
α-helix	306-316	11
α-helix	320-322	3
β-strand	324-328	5	2
α-helix	334-348	15
α-helix	351-353	3
α-helix	355-357	3
α-helix	358-362	5
α-helix	363-366	4
α-helix	367-380	14
α-helix	385-388	4
α-helix	390-392	3
α-helix	398-403	6

Chain B: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	8
β-strand	11-13	3	9
α-helix	16-18	3
α-helix	37-48	12
α-helix	50-53	4
β-strand	55-57	3	9
α-helix	58	1
α-helix	61-63	3
α-helix	64-67	4
α-helix	73-80	8
α-helix	117-142	26
β-strand	148	1	8
β-strand	149-151	3	9
β-strand	161	1	10
β-strand	164	1	10
β-strand	166	1	11
β-strand	169	1	11
α-helix	173-185	13
β-strand	190-194	5	9
α-helix	201-206	6
β-strand	213-220	8	9
α-helix	239-241	3
β-strand	245-250	6	9
β-strand	259	1	12
α-helix	260-266	7
α-helix	267-271	5
α-helix	272-278	7
β-strand	282-287	6	9
β-strand	292	1	13
β-strand	303	1	12
β-strand	304	1	13
α-helix	306-316	11
α-helix	320-322	3
β-strand	324-328	5	9
α-helix	334-348	15
α-helix	351-357	7
α-helix	358-362	5
α-helix	363-366	4
α-helix	367-380	14
α-helix	385-388	4
α-helix	390-392	3
α-helix	398-401	4

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>2VQV_1 HISTONE DEACETYLASE 4 (chains A, B)
GAMTKPRFTTGLVYDTLMLKHQCTAGSSSSHPEHAGRIQSIWSRLQETGLRGKCEAIRGR
KATLEELQTVHSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNE
VHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKL
LQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGP
GVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLG
GYNLSARCFGYLTKQLMGLAGGRIVLALEGGYDLTAICDASEACVSALLGNELDPLPEKV
LQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEAETVT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
HA3	N-hydroxy-5-[(3-phenyl-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl)carbonyl]thiop…	C18 H16 N4 O3 S	2

Water and common crystallization additives (K, SO4) 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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