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Yorodumi- PDB-5wmt: Structure of GRP94 N-terminal Domain bound to resorcinylic inhibi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wmt | |||||||||
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Title | Structure of GRP94 N-terminal Domain bound to resorcinylic inhibitor BnIm. | |||||||||
Components | Endoplasmin | |||||||||
Keywords | Chaperone/Inhibitor / Chaperone / Inhibitor / Complex / 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: 2.748 Å | |||||||||
Authors | Que, N.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 | 5wmt.cif.gz | 183.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wmt.ent.gz | 145 KB | Display | PDB format |
PDBx/mmJSON format | 5wmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wmt_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5wmt_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5wmt_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 5wmt_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/5wmt ftp://data.pdbj.org/pub/pdb/validation_reports/wm/5wmt | HTTPS FTP |
-Related structure data
Related structure data | 5vyyC 6bawC 6c91C 6ceoC 1u0zS 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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Unit cell |
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-Components
#1: Protein | Mass: 26514.012 Da / Num. of mol.: 4 / Mutation: residues 287-327 are replaced with GGGG 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 #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-9QY / #4: Chemical | #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: 3.78 Å3/Da / Density % sol: 67.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 2000, Lithium sulfate, Sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→34.544 Å / Num. obs: 49257 / % possible obs: 98.1 % / Redundancy: 4.8 % / Rsym value: 0.059 / Net I/σ(I): 34.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1u0z Resolution: 2.748→34.544 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.748→34.544 Å
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Refine LS restraints |
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LS refinement shell |
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