+Open data
-Basic information
Entry | Database: PDB / ID: 6vh4 | ||||||
---|---|---|---|---|---|---|---|
Title | Wild type EGFR in complex with LN2380 | ||||||
Components | Epidermal growth factor receptor | ||||||
Keywords | TRANSFERASE/TRANSFERASE inhibitor / Epidermal growth factor receptor / inhibitor / cancer / TRANSFERASE / 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: 2.8 Å | ||||||
Authors | Heppner, D.E. / Eck, M.J. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Structural Basis for EGFR Mutant Inhibition by Trisubstituted Imidazole Inhibitors. Authors: Heppner, D.E. / Gunther, M. / Wittlinger, F. / Laufer, S.A. / Eck, M.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6vh4.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vh4.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vh4_validation.pdf.gz | 343.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6vh4_full_validation.pdf.gz | 346.9 KB | Display | |
Data in XML | 6vh4_validation.xml.gz | 2 KB | Display | |
Data in CIF | 6vh4_validation.cif.gz | 5.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/6vh4 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/6vh4 | HTTPS FTP |
-Related structure data
Related structure data | 6v5nC 6v5pC 6v66C 6v6kC 6v6oC 6vhnC 6vhpC 6d8eS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37304.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P00533, receptor protein-tyrosine kinase |
---|---|
#2: Chemical | ChemComp-QQM / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 65 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.4 M Sodium Citrate, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.978801 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 13, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→39.17 Å / Num. obs: 12526 / % possible obs: 96.7 % / Redundancy: 5.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.056 / Rrim(I) all: 0.134 / Net I/σ(I): 9.3 / Num. measured all: 65862 / Scaling rejects: 57 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6d8e Resolution: 2.8→39.16 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.32 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.7 Å2 / Biso mean: 58.1335 Å2 / Biso min: 18.92 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→39.16 Å
| |||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
|