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Yorodumi- PDB-8hva: Crystal structure of EGFR_TMX in complex with covalently bound co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hva | ||||||
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Title | Crystal structure of EGFR_TMX in complex with covalently bound compound 14 | ||||||
Components | Epidermal growth factor receptor | ||||||
Keywords | TRANSFERASE / Epidermal growth factor receptor kinase / covalent fragments / mutant EGFR / anti-cancer | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | ||||||
Authors | Takahashi, M. / Dokurno, P. | ||||||
Funding support | 1items
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Citation | Journal: Rsc Med Chem / Year: 2023 Title: A covalent fragment-based strategy targeting a novel cysteine to inhibit activity of mutant EGFR kinase. Authors: Kuki, N. / Walmsley, D.L. / Kanai, K. / Takechi, S. / Yoshida, M. / Murakami, R. / Takano, K. / Tominaga, Y. / Takahashi, M. / Ito, S. / Nakao, N. / Angove, H. / Baker, L.M. / Carter, E. / ...Authors: Kuki, N. / Walmsley, D.L. / Kanai, K. / Takechi, S. / Yoshida, M. / Murakami, R. / Takano, K. / Tominaga, Y. / Takahashi, M. / Ito, S. / Nakao, N. / Angove, H. / Baker, L.M. / Carter, E. / Dokurno, P. / Le Strat, L. / Macias, A.T. / Molyneaux, C.A. / Murray, J.B. / Surgenor, A.E. / Hamada, T. / Hubbard, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hva.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hva.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 8hva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/8hva ftp://data.pdbj.org/pub/pdb/validation_reports/hv/8hva | HTTPS FTP |
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-Related structure data
Related structure data | 8hv1C 8hv2C 8hv3C 8hv4C 8hv5C 8hv6C 8hv7C 8hv8C 8hv9C 5edqS S: Starting model for refinement C: citing same article (ref.) |
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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: 37533.332 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 |
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#2: Chemical | ChemComp-N9R / ~{ |
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: 3.39 Å3/Da / Density % sol: 63.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M TRIS pH 8.5, 0.15M Sodium citrate, 25%PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.540562 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.540562 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→14.93 Å / Num. obs: 12847 / % possible obs: 99 % / Redundancy: 6.1 % / CC1/2: 0.989 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.106 / Rrim(I) all: 0.269 / Χ2: 1.02 / Net I/σ(I): 7.8 / Num. measured all: 78307 |
Reflection shell | Resolution: 2.77→2.92 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.621 / Num. unique obs: 1879 / CC1/2: 0.433 / Rpim(I) all: 1.059 / Rrim(I) all: 2.835 / Χ2: 0.79 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EDQ Resolution: 2.77→14.93 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.977 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R: 0.655 / ESU R Free: 0.315 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.759 Å2
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Refinement step | Cycle: 1 / Resolution: 2.77→14.93 Å
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Refine LS restraints |
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