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Yorodumi- PDB-4jr3: Crystal structure of EGFR kinase domain in complex with compound 3g -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jr3 | ||||||
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Title | Crystal structure of EGFR kinase domain in complex with compound 3g | ||||||
Components | Epidermal growth factor receptor | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Transferase / tyrosine kinase domain / ATP-binding domain / autophosphorylation / TRANSFERASE-TRANSFERASE 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: 2.7 Å | ||||||
Authors | Peng, Y.H. / Wu, J.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Protein Kinase Inhibitor Design by Targeting the Asp-Phe-Gly (DFG) Motif: The Role of the DFG Motif in the Design of Epidermal Growth Factor Receptor Inhibitors Authors: Peng, Y.H. / Shiao, H.Y. / Tu, C.H. / Liu, P.M. / Hsu, J.T. / Amancha, P.K. / Wu, J.S. / Coumar, M.S. / Chen, C.H. / Wang, S.Y. / Lin, W.H. / Sun, H.Y. / Chao, Y.S. / Lyu, P.C. / Hsieh, H.P. / Wu, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jr3.cif.gz | 137.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jr3.ent.gz | 107.6 KB | Display | PDB format |
PDBx/mmJSON format | 4jr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jr3_validation.pdf.gz | 811 KB | Display | wwPDB validaton report |
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Full document | 4jr3_full_validation.pdf.gz | 814.1 KB | Display | |
Data in XML | 4jr3_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 4jr3_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/4jr3 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/4jr3 | HTTPS FTP |
-Related structure data
Related structure data | 4jq7C 4jq8C 4jrvC 1m17S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37401.250 Da / Num. of mol.: 1 / Fragment: EGFR kinase domain, UNP residues 696-1021 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR / Plasmid: pBacPAK-MT-EGFP / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P00533, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-KJR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.0M Ammonium citrate tribase, 0.1M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 14311 / Num. obs: 14311 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.92 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1399 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1M17 Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.917 / SU B: 22.491 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.484 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.385 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 58.445 Å / Origin y: 23.961 Å / Origin z: 9.65 Å
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