+Open data
-Basic information
Entry | Database: PDB / ID: 4lxz | ||||||
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Title | Structure of Human HDAC2 in complex with SAHA (vorinostat) | ||||||
Components | Histone deacetylase 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / deacetylase / Histone / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information protein de-2-hydroxyisobutyrylase activity / positive regulation of male mating behavior / negative regulation of peptidyl-lysine acetylation / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / negative regulation of dendritic spine development / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol / negative regulation of MHC class II biosynthetic process ...protein de-2-hydroxyisobutyrylase activity / positive regulation of male mating behavior / negative regulation of peptidyl-lysine acetylation / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / negative regulation of dendritic spine development / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol / negative regulation of MHC class II biosynthetic process / NuRD complex / positive regulation of interleukin-1 production / regulation of cell fate specification / negative regulation of stem cell population maintenance / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of transcription by competitive promoter binding / ESC/E(Z) complex / regulation of stem cell differentiation / STAT3 nuclear events downstream of ALK signaling / cellular response to dopamine / histone deacetylase / cardiac muscle hypertrophy / protein lysine deacetylase activity / positive regulation of signaling receptor activity / response to caffeine / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / embryonic digit morphogenesis / positive regulation of oligodendrocyte differentiation / positive regulation of stem cell population maintenance / Sin3-type complex / Notch-HLH transcription pathway / dendrite development / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / positive regulation of proteolysis / RNA Polymerase I Transcription Initiation / response to amyloid-beta / histone deacetylase complex / hair follicle placode formation / Regulation of MECP2 expression and activity / NF-kappaB binding / positive regulation of collagen biosynthetic process / response to hyperoxia / positive regulation of epithelial to mesenchymal transition / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / heterochromatin formation / MECP2 regulates neuronal receptors and channels / cellular response to retinoic acid / positive regulation of tyrosine phosphorylation of STAT protein / Regulation of TP53 Activity through Acetylation / cellular response to transforming growth factor beta stimulus / response to amphetamine / heat shock protein binding / SUMOylation of chromatin organization proteins / negative regulation of cell migration / response to cocaine / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / response to nicotine / Regulation of PTEN gene transcription / promoter-specific chromatin binding / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / protein modification process / NoRC negatively regulates rRNA expression / negative regulation of DNA-binding transcription factor activity / NOTCH1 Intracellular Domain Regulates Transcription / cellular response to hydrogen peroxide / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / positive regulation of tumor necrosis factor production / negative regulation of neuron projection development / cellular response to heat / Factors involved in megakaryocyte development and platelet production / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / response to lipopolysaccharide / chromosome, telomeric region / chromatin remodeling / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / chromatin / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Fong, R. / Lupardus, P.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability. Authors: Lauffer, B.E. / Mintzer, R. / Fong, R. / Mukund, S. / Tam, C. / Zilberleyb, I. / Flicke, B. / Ritscher, A. / Fedorowicz, G. / Vallero, R. / Ortwine, D.F. / Gunzner, J. / Modrusan, Z. / ...Authors: Lauffer, B.E. / Mintzer, R. / Fong, R. / Mukund, S. / Tam, C. / Zilberleyb, I. / Flicke, B. / Ritscher, A. / Fedorowicz, G. / Vallero, R. / Ortwine, D.F. / Gunzner, J. / Modrusan, Z. / Neumann, L. / Koth, C.M. / Lupardus, P.J. / Kaminker, J.S. / Heise, C.E. / Steiner, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lxz.cif.gz | 259.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lxz.ent.gz | 205.5 KB | Display | PDB format |
PDBx/mmJSON format | 4lxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/4lxz ftp://data.pdbj.org/pub/pdb/validation_reports/lx/4lxz | HTTPS FTP |
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-Related structure data
Related structure data | 4ly1C 3maxS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 42367.234 Da / Num. of mol.: 3 / Fragment: core domain (UNP residues 8-376) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92769, histone deacetylase |
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-Non-polymers , 7 types, 944 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PG4 / #6: Chemical | #7: Chemical | ChemComp-NHE / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.1M CHES, pH 9.5, 40% PEG-600, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 105047 / % possible obs: 98.1 % / Redundancy: 3 % / Biso Wilson estimate: 18.25 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 1.9 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3MAX Resolution: 1.85→27.09 Å / Cor.coef. Fo:Fc: 0.9544 / Cor.coef. Fo:Fc free: 0.9412 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 20.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.171 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→27.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.9 Å / Total num. of bins used: 20
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