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- PDB-6cef: Crystal structure of fragment 3-(1,3-Benzothiazol-2-yl)propanoic ... -

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Basic information

Entry
Database: PDB / ID: 6cef
TitleCrystal structure of fragment 3-(1,3-Benzothiazol-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / HISTONE DEACETYLASE / HDAC / HDAC6 / UBIQUITIN / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / positive regulation of protein oligomerization / negative regulation of axon extension involved in axon guidance ...negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / positive regulation of protein oligomerization / negative regulation of axon extension involved in axon guidance / regulation of microtubule-based movement / type 2 mitophagy / negative regulation of protein-containing complex disassembly / peroxidase inhibitor activity / regulation of establishment of protein localization / protein-containing complex disassembly / regulation of autophagy of mitochondrion / tubulin deacetylation / Cilium Assembly / collateral sprouting / Transcriptional regulation by RUNX2 / lysosome localization / negative regulation of microtubule depolymerization / tubulin deacetylase activity / positive regulation of dendrite morphogenesis / ATPase inhibitor activity / cilium disassembly / misfolded protein binding / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / positive regulation of type 2 mitophagy / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / dendritic spine morphogenesis / histone H4K12 deacetylase activity, hydrolytic mechanism / protein deacetylation / histone H3K9 deacetylase activity, hydrolytic mechanism / aggresome assembly / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / cellular response to misfolded protein / Transferases; Acyltransferases; Aminoacyltransferases / regulation of fat cell differentiation / protein lysine deacetylase activity / microtubule associated complex / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / aggresome / positive regulation of intracellular estrogen receptor signaling pathway / cellular response to parathyroid hormone stimulus / response to corticosterone / histone deacetylase activity / negative regulation of gene expression, epigenetic / Notch-HLH transcription pathway / axonal transport of mitochondrion / dynein complex binding / beta-tubulin binding / protein quality control for misfolded or incompletely synthesized proteins / RUNX2 regulates osteoblast differentiation / cell leading edge / response to dexamethasone / histone deacetylase complex / response to immobilization stress / positive regulation of epithelial cell migration / polyubiquitin modification-dependent protein binding / cilium assembly / alpha-tubulin binding / regulation of macroautophagy / HSF1 activation / negative regulation of protein-containing complex assembly / inclusion body / axon cytoplasm / multivesicular body / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / actin filament organization / epigenetic regulation of gene expression / ubiquitin binding / transcription corepressor binding / negative regulation of proteolysis / intracellular protein transport / Hsp90 protein binding / Late endosomal microautophagy / protein destabilization / regulation of protein stability / beta-catenin binding / tau protein binding / caveola / epidermal growth factor receptor signaling pathway / regulation of autophagy / NOTCH1 Intracellular Domain Regulates Transcription / cellular response to hydrogen peroxide / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Chaperone Mediated Autophagy / protein polyubiquitination / Aggrephagy / actin binding
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Zinc/RING finger domain, C3HC4 (zinc finger) ...Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(1,3-benzothiazol-2-yl)propanoic acid / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsHarding, R.J. / Halabelian, L. / Ferreira de Freitas, R. / Ravichandran, M. / Santhakumar, V. / Schapira, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.M. / Structural Genomics Consortium (SGC)
CitationJournal: J. Med. Chem. / Year: 2018
Title: Identification and Structure-Activity Relationship of HDAC6 Zinc-Finger Ubiquitin Binding Domain Inhibitors.
Authors: Ferreira de Freitas, R. / Harding, R.J. / Franzoni, I. / Ravichandran, M. / Mann, M.K. / Ouyang, H. / Lautens, M. / Santhakumar, V. / Arrowsmith, C.H. / Schapira, M.
History
DepositionFeb 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3368
Polymers11,9331
Non-polymers4037
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.700, 44.210, 56.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone deacetylase 6 / HD6


Mass: 11932.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC6, KIAA0901, JM21 / Plasmid: pET28-lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: Q9UBN7, histone deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Chemical ChemComp-EYJ / 3-(1,3-benzothiazol-2-yl)propanoic acid


Mass: 207.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.07 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→34.71 Å / Num. obs: 9350 / % possible obs: 95.5 % / Redundancy: 7.2 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.017 / Rrim(I) all: 0.045 / Net I/σ(I): 38.4 / Num. measured all: 67104
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.847.40.14339405340.9930.0560.15413.291.1
9-34.715.20.0245039710.0110.02677.998.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementStarting model: pdbid 5KH3

5kh3


Resolution: 1.8→34.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.929 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 447 4.8 %RANDOM
Rwork0.1501 ---
obs0.1515 8903 94.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.07 Å2 / Biso mean: 12.606 Å2 / Biso min: 6.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å2-0 Å20 Å2
2--2.16 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: final / Resolution: 1.8→34.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms779 0 20 90 889
Biso mean--19.23 21.79 -
Num. residues----100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019850
X-RAY DIFFRACTIONr_bond_other_d0.0030.02698
X-RAY DIFFRACTIONr_angle_refined_deg1.841.9141169
X-RAY DIFFRACTIONr_angle_other_deg1.2383.011620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3935103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09424.61539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.57815111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.674151
X-RAY DIFFRACTIONr_chiral_restr0.1320.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211017
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02172
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 26 -
Rwork0.149 631 -
all-657 -
obs--90.75 %

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