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- PDB-5fcw: HDAC8 Complexed with a Hydroxamic Acid -

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Basic information

Entry
Database: PDB / ID: 5fcw
TitleHDAC8 Complexed with a Hydroxamic Acid
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / histone deacetylase / HDAC8 / hydroxamic acid
Function / homology
Function and homology information


histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / regulation of telomere maintenance / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex ...histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / regulation of telomere maintenance / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / Hsp70 protein binding / HDACs deacetylate histones / Hsp90 protein binding / regulation of protein stability / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Separation of Sister Chromatids / chromatin organization / DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Histone deacetylase / Histone deacetylase domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-naphthalen-1-yl-~{N}-oxidanyl-benzamide / : / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 Å
AuthorsCole, K.E. / Perry, K.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structure of 'linkerless' hydroxamic acid inhibitor-HDAC8 complex confirms the formation of an isoform-specific subpocket.
Authors: Tabackman, A.A. / Frankson, R. / Marsan, E.S. / Perry, K. / Cole, K.E.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 8
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,89912
Polymers85,2632
Non-polymers1,63710
Water7,458414
1
A: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2815
Polymers42,6311
Non-polymers6504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6187
Polymers42,6311
Non-polymers9866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.443, 84.548, 94.307
Angle α, β, γ (deg.)90.00, 100.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histone deacetylase 8 / HD8


Mass: 42631.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BY41, histone deacetylase

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Non-polymers , 6 types, 424 molecules

#2: Chemical
ChemComp-5YA / 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide


Mass: 263.291 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H13NO2
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3 / Details: 4% PEG 3350, 50 mM buffer (MES, pH 5.3)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2013
RadiationMonochromator: Double Crystal Si 11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→49.67 Å / Num. obs: 107583 / % possible obs: 97.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.979→49.659 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 5464 5.08 %
Rwork0.1719 --
obs0.174 106016 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.979→49.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5591 0 96 414 6101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075861
X-RAY DIFFRACTIONf_angle_d1.0687955
X-RAY DIFFRACTIONf_dihedral_angle_d13.6682132
X-RAY DIFFRACTIONf_chiral_restr0.07860
X-RAY DIFFRACTIONf_plane_restr0.0051012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9794-2.00190.31041840.2683398X-RAY DIFFRACTION96
2.0019-2.02550.27361760.27033411X-RAY DIFFRACTION96
2.0255-2.05020.31851900.2633387X-RAY DIFFRACTION93
2.0502-2.07610.32521660.26453348X-RAY DIFFRACTION94
2.0761-2.10340.29862080.24333371X-RAY DIFFRACTION96
2.1034-2.13220.25731940.22683535X-RAY DIFFRACTION97
2.1322-2.16270.28981740.22183410X-RAY DIFFRACTION96
2.1627-2.1950.27461880.22733448X-RAY DIFFRACTION96
2.195-2.22930.30012110.2243517X-RAY DIFFRACTION97
2.2293-2.26580.22341680.21933395X-RAY DIFFRACTION97
2.2658-2.30490.26181900.20393507X-RAY DIFFRACTION97
2.3049-2.34680.2761830.20453421X-RAY DIFFRACTION97
2.3468-2.3920.23791980.19793488X-RAY DIFFRACTION97
2.392-2.44080.24541960.19823423X-RAY DIFFRACTION96
2.4408-2.49380.26961580.19013275X-RAY DIFFRACTION91
2.4938-2.55190.2661840.18823444X-RAY DIFFRACTION95
2.5519-2.61570.25521950.18363431X-RAY DIFFRACTION97
2.6157-2.68640.25441940.17393446X-RAY DIFFRACTION96
2.6864-2.76540.20651810.17533502X-RAY DIFFRACTION97
2.7654-2.85470.26561990.16863440X-RAY DIFFRACTION96
2.8547-2.95670.22261660.1693456X-RAY DIFFRACTION96
2.9567-3.07510.19951880.15993408X-RAY DIFFRACTION96
3.0751-3.2150.23431720.17533345X-RAY DIFFRACTION93
3.215-3.38450.21791970.16623314X-RAY DIFFRACTION93
3.3845-3.59640.18991620.15433424X-RAY DIFFRACTION94
3.5964-3.8740.22761670.14663359X-RAY DIFFRACTION94
3.874-4.26370.15351810.13743297X-RAY DIFFRACTION93
4.2637-4.88020.13991790.12353208X-RAY DIFFRACTION89
4.8802-6.14670.14971540.15353407X-RAY DIFFRACTION94
6.1467-49.67440.16151610.14623304X-RAY DIFFRACTION92

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