+Open data
-Basic information
Entry | Database: PDB / ID: 7c05 | ||||||
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Title | Crystal structure of human Trap1 with DN203495 | ||||||
Components | Heat shock protein 75 kDa, mitochondrialHeat shock response | ||||||
Keywords | CHAPERONE / TRAP1 / selectivity / mitochondria / Hsp90 / Anticancer / Drug | ||||||
Function / homology | Function and homology information translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space ...translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space / unfolded protein binding / protein folding / mitochondrial inner membrane / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Kim, D. / Kim, D. / Kim, S.Y. / Lee, J.H. / Kang, B.H. / Kang, S. / Lee, C. | ||||||
Citation | Journal: Bioorg.Chem. / Year: 2020 Title: Development of pyrazolo[3,4-d]pyrimidine-6-amine-based TRAP1 inhibitors that demonstrate in vivo anticancer activity in mouse xenograft models. Authors: Kim, D. / Kim, S.Y. / Kim, D. / Yoon, N.G. / Yun, J. / Hong, K.B. / Lee, C. / Lee, J.H. / Kang, B.H. / Kang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c05.cif.gz | 232.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c05.ent.gz | 155.3 KB | Display | PDB format |
PDBx/mmJSON format | 7c05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/7c05 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/7c05 | HTTPS FTP |
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-Related structure data
Related structure data | 7c04C 5y3nS 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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Unit cell |
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-Components
#1: Protein | Mass: 57422.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRAP1, HSP75 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12931 |
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#2: Chemical | ChemComp-FE6 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.76 Details: 0.1M Cacodylate pH 6.76, 0.1M Ca-acetate, 14% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 20501 / % possible obs: 99.3 % / Redundancy: 10.5 % / Biso Wilson estimate: 48.8940709925 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.521 / Num. unique obs: 20501 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y3N Resolution: 2.59→49.42 Å / SU ML: 0.357867561877 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 26.5605219153
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.1610402535 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→49.42 Å
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Refine LS restraints |
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LS refinement shell |
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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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