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- PDB-6r0k: X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 ... -

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Basic information

Entry
Database: PDB / ID: 6r0k
TitleX-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with a inhibitor SS208
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / protein deacetylase / histone deacetylase 6 / Zinc-binding / isoxazole-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 / epigenetic regulation of gene expression / angiogenesis / 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 domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily ...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 domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JNN / : / THIOCYANATE ION / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å
AuthorsBarinka, C. / Ustinova, K. / Motlova, L. / Pavlicek, J.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of a New Isoxazole-3-hydroxamate-Based Histone Deacetylase 6 Inhibitor SS-208 with Antitumor Activity in Syngeneic Melanoma Mouse Models.
Authors: Shen, S. / Hadley, M. / Ustinova, K. / Pavlicek, J. / Knox, T. / Noonepalle, S. / Tavares, M.T. / Zimprich, C.A. / Zhang, G. / Robers, M.B. / Barinka, C. / Kozikowski, A.P. / Villagra, A.
History
DepositionMar 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,85213
Polymers39,8991
Non-polymers95212
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-20 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.028, 93.886, 51.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2006-

SCN

21A-2006-

SCN

31A-2006-

SCN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone deacetylase 6


Mass: 39899.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Cell line (production host): HEKs / Production host: Homo sapiens (human) / References: UniProt: F8W4B7

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Non-polymers , 5 types, 408 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-JNN / 5-[2-[(3,4-dichlorophenyl)carbonylamino]ethyl]-~{N}-oxidanyl-1,2-oxazole-3-carboxamide


Mass: 344.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11Cl2N3O4
#5: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 19 % PEG 3350, 0.2 M KSCN, 0,1 M Bis Tris pH 6.5

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 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: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 138875 / % possible obs: 95.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.13
Reflection shellResolution: 1.15→1.22 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 21216 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
REFMACphasing
pointlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5EEK

5eek


Resolution: 1.15→46.94 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.898 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17823 2100 1.5 %RANDOM
Rwork0.17027 ---
obs0.17039 136766 95.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.587 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0 Å20 Å2
2--2.54 Å2-0 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.15→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 49 396 3209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123124
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.6314249
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14120.795176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83415508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0361526
X-RAY DIFFRACTIONr_chiral_restr0.1030.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8391.4081534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2692.0961936
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4341.5841589
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.38420.9045053
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.149→1.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 146 -
Rwork0.344 9537 -
obs--90.77 %
Refinement TLS params.Method: refined / Origin x: -16.1231 Å / Origin y: 22.7022 Å / Origin z: -4.4311 Å
111213212223313233
T0.0177 Å2-0.0003 Å2-0.0032 Å2-0.0054 Å20.0044 Å2--0.0125 Å2
L0.2202 °20.0069 °20.0044 °2-0.07 °2-0.0667 °2--0.1814 °2
S0.0121 Å °-0.0012 Å °0.0172 Å °-0.001 Å °0.0045 Å °-0.0128 Å °0.0115 Å °-0.0284 Å °-0.0166 Å °

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