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Yorodumi- PDB-6aom: Structure of molecular chaperone Grp94 bound to selective inhibit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aom | ||||||
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Title | Structure of molecular chaperone Grp94 bound to selective inhibitor methyl 2-[2-(2-benzylphenyl)ethyl]-3-chloro-4,6-dihydroxybenzoate | ||||||
Components | Endoplasmin | ||||||
Keywords | CHAPERONE/INHIBITOR / Grp94 / Hsp90 / 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: 2.87 Å | ||||||
Authors | Lieberman, R.L. / Huard, D.J.E. | ||||||
Citation | Journal: Chemistry / Year: 2017 Title: Second Generation Grp94-Selective Inhibitors Provide Opportunities for the Inhibition of Metastatic Cancer. Authors: Crowley, V.M. / Huard, D.J.E. / Lieberman, R.L. / Blagg, B.S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aom.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aom.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 6aom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aom_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 6aom_full_validation.pdf.gz | 3.9 MB | Display | |
Data in XML | 6aom_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 6aom_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/6aom ftp://data.pdbj.org/pub/pdb/validation_reports/ao/6aom | HTTPS FTP |
-Related structure data
Related structure data | 6aolC 2gfdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26187.615 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: HSP90B1, GRP94, TRA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41148 |
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-Non-polymers , 5 types, 46 molecules
#2: Chemical | ChemComp-P33 / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-PEG / | #6: 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: 2.5 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 30 mg/mL protein in 100 mM bicine, pH 7.8 mixed 1:1 with mother liquor (35-39% PEG400, 7.5-10% glycerol, 100 mM bicine, pH 7.8, 75 mM magnesium chloride, crystals harvested into mother ...Details: 30 mg/mL protein in 100 mM bicine, pH 7.8 mixed 1:1 with mother liquor (35-39% PEG400, 7.5-10% glycerol, 100 mM bicine, pH 7.8, 75 mM magnesium chloride, crystals harvested into mother liquor + 2 mM inhibitor, soaked for 4 days. Afterward, glycerol was added to 25% and crystals were harvested and immediately cryocooled with liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 197.5 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 7, 2017 |
Radiation | Monochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→35.42 Å / Num. obs: 12437 / % possible obs: 99 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.1418 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.87→2.972 Å / Rmerge(I) obs: 0.4039 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2GFD Resolution: 2.87→35.42 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.87→35.42 Å
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Refine LS restraints |
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LS refinement shell |
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