Structure of HDAC4 catalytic domain bound to a trifluoromethylketone inhbitor. Determined by X-ray diffraction at 2.1 Å resolution. Released 8 Jul 2008.
Explore 2VQJ in 3D Show helices and sheets RCSB PDB PDBe
2VQJ 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 10-14 | 5 | 1 |
| α-helix | 16-18 | 3 | |
| α-helix | 37-47 | 11 | |
| α-helix | 50-53 | 4 | |
| β-strand | 55-58 | 4 | 1 |
| α-helix | 61-63 | 3 | |
| α-helix | 64-67 | 4 | |
| α-helix | 73-80 | 8 | |
| α-helix | 83-86 | 4 | |
| α-helix | 92-101 | 10 | |
| 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 | 173-185 | 13 | |
| 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 | 306-316 | 11 | |
| α-helix | 320-322 | 3 | |
| β-strand | 324-328 | 5 | 1 |
| α-helix | 334-348 | 15 | |
| α-helix | 351-357 | 7 | |
| α-helix | 358-362 | 5 | |
| α-helix | 363-366 | 4 | |
| α-helix | 367-380 | 14 | |
| α-helix | 385-387 | 3 | |
| α-helix | 398-406 | 9 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Histone deacetylase 4 | A | protein | 413 | HOMO SAPIENS | P56524 (AlphaFold model) |
>2VQJ_1 HISTONE DEACETYLASE 4 (chains A) GAMTKPRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGR KATLEELQTVHSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNE VHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKL LQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGP GVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLG GYNLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKV LQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEAETVT
| 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 | 1 |
| DIO | 1,4-diethylene dioxide | C4 H8 O2 | 1 |
Water and common crystallization additives (SO4, K) are not listed.
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:
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