2VQQ: HDAC4 catalytic domain

Structure of HDAC4 catalytic domain (a double cysteine-to-alanine mutant) bound to a trifluoromethylketone inhbitor. Determined by X-ray diffraction at 1.9 Å resolution. Released 8 Jul 2008.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 6,218
Mol. weight: 90.25 kDa
Ligands: ZN, TFG
Released: 8 Jul 2008

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

Secondary structure: helices and β-sheets

2VQQ contains 49 α-helices and 26 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: 24 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	1
α-helix	16-18	3
α-helix	37-47	11
α-helix	50-53	4
β-strand	55-57	3	1
α-helix	58	1
α-helix	61-63	3
α-helix	64-67	4
α-helix	73-80	8
α-helix	118-142	25
β-strand	148-151	4	1
β-strand	161	1	2
β-strand	164	1	2
β-strand	166	1	3
β-strand	169	1	3
α-helix	173-185	13
β-strand	190-194	5	1
α-helix	201-206	6
β-strand	213-220	8	1
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	306-316	11
α-helix	320-322	3
β-strand	324-328	5	1
α-helix	334-348	15
α-helix	351-357	7
α-helix	358-361	4
α-helix	363-366	4
α-helix	367-380	14
α-helix	385-387	3
α-helix	398-403	6

Chain B: 25 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	5
α-helix	16-18	3
α-helix	37-47	11
α-helix	50-53	4
β-strand	55-57	3	5
α-helix	58	1
α-helix	61-63	3
α-helix	64-67	4
α-helix	73-80	8
α-helix	118-142	25
β-strand	148-151	4	5
β-strand	166	1	6
β-strand	169	1	6
α-helix	173-185	13
β-strand	190-194	5	5
α-helix	201-206	6
β-strand	213-220	8	5
α-helix	222-224	3
α-helix	239-241	3
β-strand	245-250	6	5
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	5
β-strand	292	1	7
β-strand	304	1	7
α-helix	306-316	11
α-helix	320-322	3
β-strand	324-328	5	5
α-helix	334-348	15
α-helix	351-357	7
α-helix	358-361	4
α-helix	363-366	4
α-helix	367-380	14
α-helix	385-387	3
α-helix	398-403	6

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

>2VQQ_1 HISTONE DEACETYLASE 4 (chains A, B)
GAMTKPRFTTGLVYDTLMLKHQCTAGSSSSHPEHAGRIQSIWSRLQETGLRGKCEAIRGR
KATLEELQTVHSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNE
VHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKL
LQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGP
GVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLG
GYNLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKV
LQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEAETVT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
TFG	2,2,2-trifluoro-1-{5-[(3-phenyl-5,6-DIHYDROIMIDAZO[1,2-a]pyrazin-7(8H)-yl)carbo…	C19 H16 F3 N3 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 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
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…

Browse structure collections

About this viewer

MolViewer shows 2VQQ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.