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- PDB-5aqi: Fragment-based screening of HSP70 sheds light on the functional r... -
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Basic information
Entry | Database: PDB / ID: 5aqi | ||||||
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Title | Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues | ||||||
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![]() | CHAPERONE / HEAT SHOCK PROTEIN / HSP70 / HSP72 / HSC70 / ATPASE / BAG1 / FRAGMENT | ||||||
Function / homology | ![]() lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / positive regulation of lysosomal membrane permeability / lysosomal matrix / A1 adenosine receptor binding / protein carrier chaperone / response to nickel cation ...lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / positive regulation of lysosomal membrane permeability / lysosomal matrix / A1 adenosine receptor binding / protein carrier chaperone / response to nickel cation / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Respiratory syncytial virus genome transcription / protein transmembrane import into intracellular organelle / Lipophagy / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / adenyl-nucleotide exchange factor activity / late endosomal microautophagy / response to odorant / positive regulation by host of viral genome replication / synaptic vesicle uncoating / C3HC4-type RING finger domain binding / positive regulation of smooth muscle cell apoptotic process / negative regulation of NLRP3 inflammasome complex assembly / clathrin coat disassembly / CHL1 interactions / ATP-dependent protein disaggregase activity / regulation of protein complex stability / photoreceptor ribbon synapse / maintenance of postsynaptic specialization structure / membrane organization / Prp19 complex / glycinergic synapse / presynaptic cytosol / postsynaptic specialization membrane / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic cytosol / regulation of postsynapse organization / negative regulation of cardiac muscle cell apoptotic process / Lysosome Vesicle Biogenesis / intermediate filament / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / Golgi Associated Vesicle Biogenesis / phosphatidylserine binding / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / positive regulation of proteolysis / HSF1-dependent transactivation / response to unfolded protein / estrous cycle / Regulation of HSF1-mediated heat shock response / autophagosome / regulation of protein-containing complex assembly / Attenuation phase / Protein methylation / protein folding chaperone / ATP metabolic process / positive regulation of phagocytosis / skeletal muscle tissue development / forebrain development / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to cadmium ion / cellular response to starvation / photoreceptor inner segment / lysosomal lumen / mRNA Splicing - Major Pathway / cerebellum development / dendritic shaft / response to activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / kidney development / G protein-coupled receptor binding / response to progesterone / ATP-dependent protein folding chaperone / peptide binding / Late endosomal microautophagy / spliceosomal complex / PKR-mediated signaling / regulation of protein stability / terminal bouton / ADP binding / mRNA splicing, via spliceosome / Chaperone Mediated Autophagy / cellular response to hydrogen peroxide / G1/S transition of mitotic cell cycle / positive regulation of T cell mediated cytotoxicity / protein import into nucleus / unfolded protein binding / melanosome / protein folding / late endosome / synaptic vesicle / response to estradiol / MHC class II protein complex binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. ...Jones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. / Liu, M. / Richards, M. / McAndrew, C. / Yahya, N. / Dobson, S.E. / Jones, K. / Workman, P. / Collins, I. / van Montfort, R.L.M. | ||||||
![]() | ![]() Title: A fragment-based approach applied to a highly flexible target: Insights and challenges towards the inhibition of HSP70 isoforms. Authors: Jones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. / Liu, M. / Richards, M. / McAndrew, C. / ...Authors: Jones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. / Liu, M. / Richards, M. / McAndrew, C. / Yahya, N. / Dobson, S.E. / Jones, K. / Workman, P. / Collins, I. / van Montfort, R.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 388.4 KB | Display | ![]() |
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PDB format | ![]() | 319.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.8 KB | Display | ![]() |
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Full document | ![]() | 495.2 KB | Display | |
Data in XML | ![]() | 37.1 KB | Display | |
Data in CIF | ![]() | 52.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5aqfC ![]() 5aqgC ![]() 5aqhC ![]() 5aqjC ![]() 5aqkC ![]() 5aqlC ![]() 5aqmC ![]() 5aqnC ![]() 5aqoC ![]() 5aqpC ![]() 5aqqC ![]() 5aqrC ![]() 5aqsC ![]() 5aqtC ![]() 5aquC ![]() 5aqvC ![]() 5aqwC ![]() 5aqxC ![]() 5aqyC ![]() 1hx1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 42406.980 Da / Num. of mol.: 2 / Fragment: NUCLEOTIDE BINDING DOMAIN, RESIDUES 1-381 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 13511.571 Da / Num. of mol.: 2 / Fragment: RESIDUES 222-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 271 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ADE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
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#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.65 % / Description: COMPLETENESS IN INNER SHELL 97.8 |
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Crystal grow | pH: 8.5 Details: 16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9775 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→40.96 Å / Num. obs: 34725 / % possible obs: 45.7 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 20.88 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 0.5 / % possible all: 13 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HX1 Resolution: 1.98→40.96 Å / Cor.coef. Fo:Fc: 0.9333 / Cor.coef. Fo:Fc free: 0.8758 / SU R Cruickshank DPI: 0.691 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.706 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.297 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 30.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.268 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→40.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.04 Å / Total num. of bins used: 17
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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