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Yorodumi- PDB-8kfq: The crystal structure of EGFR(T797M/L858R) with small molecule in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8kfq | ||||||
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Title | The crystal structure of EGFR(T797M/L858R) with small molecule inhibitor B6 | ||||||
Components | Epidermal growth factor receptor | ||||||
Keywords | SIGNALING PROTEIN/INHIBITOR / inhibitor / complex / kinase / SIGNALING PROTEIN / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information Complex I biogenesis / Respiratory electron transport / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / NADH dehydrogenase (ubiquinone) activity / aerobic respiration / electron transfer activity / mitochondrial inner membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å | ||||||
Authors | Wu, C. / Ouyang, L. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of EGFR(T979M/L858R) with small molecule inhibitor B6 Authors: Wu, C. / Ouyang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kfq.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kfq.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 8kfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/8kfq ftp://data.pdbj.org/pub/pdb/validation_reports/kf/8kfq | HTTPS FTP |
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-Related structure data
Related structure data | 3ikaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36910.781 Da / Num. of mol.: 1 / Mutation: T797M,L858R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00533 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-VUZ / ~{ Mass: 433.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20ClN7O / Feature type: SUBJECT OF INVESTIGATION |
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: 3.71 Å3/Da / Density % sol: 66.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES, pH 7.0, 10% (W/V) PEG10000, 10%(V/V) Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 3.22→29.7 Å / Num. obs: 8437 / % possible obs: 89.6 % / Redundancy: 20 % / CC1/2: 0.99 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 3.22→3.31 Å / Num. unique obs: 23665 / CC1/2: 0.449 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IKA Resolution: 3.22→28.53 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8 / 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: 3.22→28.53 Å
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Refine LS restraints |
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LS refinement shell |
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