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Yorodumi- PDB-8dnk: Crystal structure of human KRAS G12C covalently bound with Taiho ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dnk | ||||||
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Title | Crystal structure of human KRAS G12C covalently bound with Taiho WO2020/085493A1 compound 6 | ||||||
Components | Isoform 2B of GTPase KRas | ||||||
Keywords | SIGNALING PROTEIN / Inhibitor / GTPase | ||||||
Function / homology | small monomeric GTPase / Ca2+ pathway / GUANOSINE-5'-DIPHOSPHATE / Chem-U50 / Isoform 2B of GTPase KRas Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Mohr, C. | ||||||
Funding support | 1items
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Citation | Journal: J.Comput.Aided Mol.Des. / Year: 2022 Title: Modeling receptor flexibility in the structure-based design of KRAS G12C inhibitors. Authors: Zhu, K. / Li, C. / Wu, K.Y. / Mohr, C. / Li, X. / Lanman, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dnk.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dnk.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 8dnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dnk_validation.pdf.gz | 992.9 KB | Display | wwPDB validaton report |
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Full document | 8dnk_full_validation.pdf.gz | 1007.9 KB | Display | |
Data in XML | 8dnk_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 8dnk_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/8dnk ftp://data.pdbj.org/pub/pdb/validation_reports/dn/8dnk | HTTPS FTP |
-Related structure data
Related structure data | 8dniC 8dnjC 6oimS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21133.867 Da / Num. of mol.: 1 / Mutation: C51S,C80L,C118S Source method: isolated from a genetically manipulated source Details: G12C variant / Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Variant: VAR_006839 G12C / Production host: Escherichia coli (E. coli) / References: UniProt: P01116-2, small monomeric GTPase |
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-Non-polymers , 5 types, 46 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-GDP / |
#4: Chemical | ChemComp-U50 / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS pH 8.5, 2.0 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2020 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→64.48 Å / Num. obs: 12603 / % possible obs: 100 % / Redundancy: 38.4 % / CC1/2: 0.998 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.23→2.27 Å / Redundancy: 40.1 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 627 / CC1/2: 0.757 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6OIM Resolution: 2.23→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.7 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 119.75 Å2 / Biso mean: 39.259 Å2 / Biso min: 20.39 Å2
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Refinement step | Cycle: final / Resolution: 2.23→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.231→2.289 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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