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- PDB-7plk: Crystal structure bovine Hsc70(aa1-554)E213A/D214A in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7plk | ||||||
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Title | Crystal structure bovine Hsc70(aa1-554)E213A/D214A in complex with nicotinic-acid-derivative | ||||||
![]() | Heat shock cognate 71 kDa protein | ||||||
![]() | CHAPERONE | ||||||
Function / homology | ![]() Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport ...Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / synaptic vesicle uncoating / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Prp19 complex / presynaptic cytosol / postsynaptic cytosol / Neutrophil degranulation / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / autophagosome / protein folding chaperone / heat shock protein binding / RNA splicing / ATP-dependent protein folding chaperone / spliceosomal complex / terminal bouton / mRNA processing / melanosome / protein-macromolecule adaptor activity / protein refolding / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / dendrite / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zehe, M. / Grimm, C. / Sotriffer, C. | ||||||
![]() | ![]() Title: Combined In-Solution Fragment Screening and Crystallographic Binding-Mode Analysis with a Two-Domain Hsp70 Construct. Authors: Zehe, M. / Kehrein, J. / Schollmayer, C. / Plank, C. / Kovacs, H. / Merino Asumendi, E. / Holzgrabe, U. / Grimm, C. / Sotriffer, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 250.9 KB | Display | ![]() |
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PDB format | ![]() | 177.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 744.2 KB | Display | ![]() |
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Full document | ![]() | 753.1 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6h54C ![]() 7o6rC ![]() 7odbC ![]() 7oddC ![]() 7odiC ![]() 4fl9S C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60978.867 Da / Num. of mol.: 1 / Mutation: E213A, D214A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 90 molecules ![](data/chem/img/7UE.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-7UE / |
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#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-EPE / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.45 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 7.5 Details: PEG 8000, TMAO, potassium chloride, HEPES-NaOH, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.4878→50 Å / Num. obs: 19088 / % possible obs: 98.19 % / Redundancy: 6.6 % / Biso Wilson estimate: 40.05 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1852 / Rpim(I) all: 0.07733 / Rrim(I) all: 0.2011 / Net I/av σ(I): 7.83 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.488→2.577 Å / Rmerge(I) obs: 1.643 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 1741 / CC1/2: 0.578 / CC star: 0.856 / Rpim(I) all: 0.6779 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FL9 Resolution: 2.4878136608→50 Å / SU ML: 0.381428449647 / Cross valid method: FREE R-VALUE / σ(F): 1.33753367553 / Phase error: 31.2617600946 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.8195741819 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4878136608→50 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -20.3946875272 Å / Origin y: -10.3743821943 Å / Origin z: -22.1637177435 Å
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Refinement TLS group | Selection details: all |