2VQM: HDAC4 catalytic domain

Structure of HDAC4 catalytic domain bound to a hydroxamic acid inhbitor. Determined by X-ray diffraction at 1.8 Å resolution. Released 8 Jul 2008.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 3,330
Mol. weight: 45.05 kDa
Ligands: ZN, HA3
Released: 8 Jul 2008

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

Secondary structure: helices and β-sheets

2VQM contains 25 α-helices and 16 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 A: 25 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	1
α-helix	16-18	3
α-helix	37-48	12
α-helix	50-53	4
β-strand	55-57	3	1
α-helix	61-63	3
α-helix	64-67	4
α-helix	73-80	8
α-helix	83-86	4
α-helix	93-101	9
β-strand	102-104	3	2
β-strand	110-112	3	2
α-helix	118-142	25
β-strand	148-151	4	1
β-strand	161	1	3
β-strand	164	1	3
β-strand	166	1	4
β-strand	169	1	4
α-helix	173-184	12
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	260-266	7
α-helix	267-271	5
α-helix	272-278	7
β-strand	282-287	6	1
β-strand	292	1	5
β-strand	304	1	5
α-helix	306-317	12
α-helix	320-322	3
β-strand	324-328	5	1
α-helix	334-348	15
α-helix	351-357	7
α-helix	358-362	5
α-helix	363-366	4
α-helix	367-381	15
α-helix	385-387	3
α-helix	398-403	6

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>2VQM_1 HISTONE DEACETYLASE 4 (chains A)
GAMTKPRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGR
KATLEELQTVHSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNE
VHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKL
LQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGP
GVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLG
GYNLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKV
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	1

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

Primary citation

Structural and Functional Analysis of the Human Hdac4 Catalytic Domain Reveals a Regulatory 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…
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…
5ZOP 2.7 Å, Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor…

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