+Open data
-Basic information
Entry | Database: PDB / ID: 6baw | |||||||||
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Title | Structure of GRP94 with a selective resorcinylic inhibitor. | |||||||||
Components | Endoplasmin | |||||||||
Keywords | CHAPERONE/INHIBITOR / CHAPERONE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / unfolded protein binding / melanosome ...Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / unfolded protein binding / melanosome / protein folding / response to heat / DNA damage response / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | Canis lupus familiaris (dog) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å | |||||||||
Authors | Que, N.L.S. / Gewirth, D.T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Med. Chem. / Year: 2018 Title: Structure Based Design of a Grp94-Selective Inhibitor: Exploiting a Key Residue in Grp94 To Optimize Paralog-Selective Binding. Authors: Que, N.L.S. / Crowley, V.M. / Duerfeldt, A.S. / Zhao, J. / Kent, C.N. / Blagg, B.S.J. / Gewirth, D.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6baw.cif.gz | 186.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6baw.ent.gz | 148.4 KB | Display | PDB format |
PDBx/mmJSON format | 6baw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/6baw ftp://data.pdbj.org/pub/pdb/validation_reports/ba/6baw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26514.012 Da / Num. of mol.: 4 Mutation: RESIDUES 287-327 DELETED AND REPLACED WITH 4 GLYCINES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: HSP90B1, GRP94, TRA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41148 #2: Chemical | ChemComp-D57 / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PO4 / #5: 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: 3.63 Å3/Da / Density % sol: 66.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Peg 2000 MME, Ammonium phosphate, Sodium Cacodylate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0333 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0333 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 41640 / % possible obs: 96.8 % / Redundancy: 5.9 % / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.7→2.75 Å / Num. measured obs: 2119 / Rsym value: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.703→41.903 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.703→41.903 Å
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Refine LS restraints |
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LS refinement shell |
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