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- PDB-6tcy: X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 ... -

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Basic information

Entry
Database: PDB / ID: 6tcy
TitleX-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with a inhibitor SS555
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / PROTEIN DEACETYLASE / HISTONE DEACETYLASE 6 / ZINC-BINDING / ISOXAZOLE-2 3-HYDROXAMATE ANALOGUES
Function / homology
Function and homology information


Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation ...Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / angiogenesis / negative regulation of transcription by RNA polymerase II / zinc ion 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 / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / 2-METHOXYETHANOL / Chem-N28 / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsStransky, J. / Barinka, C.
Funding support Czech Republic, 4items
OrganizationGrant numberCountry
Czech Science Foundation15-19640S Czech Republic
Czech Academy of Sciences86652036 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0109 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2015043 Czech Republic
CitationJournal: J.Med.Chem. / Year: 2020
Title: Rational Design of Suprastat: A Novel Selective Histone Deacetylase 6 Inhibitor with the Ability to Potentiate Immunotherapy in Melanoma Models.
Authors: Noonepalle, S. / Shen, S. / Ptacek, J. / Tavares, M.T. / Zhang, G. / Stransky, J. / Pavlicek, J. / Ferreira, G.M. / Hadley, M. / Pelaez, G. / Barinka, C. / Kozikowski, A.P. / Villagra, A.
History
DepositionNov 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Histone deacetylase 6
BBB: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,73922
Polymers79,7982
Non-polymers1,94120
Water13,655758
1
AAA: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,03113
Polymers39,8991
Non-polymers1,13212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7089
Polymers39,8991
Non-polymers8088
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.809, 83.811, 86.092
Angle α, β, γ (deg.)90, 97.971, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Histone deacetylase 6


Mass: 39899.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues at the sequence begining are not visible in the maps
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: F8W4B7

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Non-polymers , 10 types, 778 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-N28 / 4-[[[4-(aminomethyl)phenyl]carbamoyl-(4-oxidanylbutyl)amino]methyl]-~{N}-oxidanyl-benzamide


Mass: 386.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#10: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.4336634 Å3/Da / Density % sol: 49.490314 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis Tris, 0,2 M KSCN, 16% PEG 3350 Protein stock buffer: 5% DMSO, 0.004M SS555, 0.05 M Hepes pH 7.5, 0.001M TCEP, 5% v/v glycerol, 0.1M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 16, 2019
RadiationMonochromator: Si111 DCM with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→85.26 Å / Num. obs: 100361 / % possible obs: 98.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 12.16 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.095 / Rrim(I) all: 0.179 / Net I/σ(I): 6.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.056 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5038 / CC1/2: 0.612 / Rpim(I) all: 0.693 / Rrim(I) all: 1.27 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5eek

5eek


Resolution: 1.6→54.34 Å / Cross valid method: FREE R-VALUE / σ(F): -3
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4983 5 %Random selection
Rwork0.191 ---
obs0.192 99303 98.8 %-
Displacement parametersBiso mean: 15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→54.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 117 758 6455

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