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- PDB-7rp3: Crystal structure of GNE-1952 alkylated KRAS G12C in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rp3 | ||||||
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Title | Crystal structure of GNE-1952 alkylated KRAS G12C in complex with 2H11 CLAMP | ||||||
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![]() | Hydrolase/Immune System / GTPase / inhibitor / conformation-specific antibody / Hydrolase-Immune System complex | ||||||
Function / homology | small monomeric GTPase / Ca2+ pathway / GUANOSINE-5'-DIPHOSPHATE / Chem-MKZ / Isoform 2B of GTPase KRas![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oh, A. / Tam, C. / Wang, W. | ||||||
Funding support | 1items
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![]() | ![]() Title: Conformation-locking antibodies for the discovery and characterization of KRAS inhibitors. Authors: Davies, C.W. / Oh, A.J. / Mroue, R. / Steffek, M. / Bruning, J.M. / Xiao, Y. / Feng, S. / Jayakar, S. / Chan, E. / Arumugam, V. / Uribe, S.C. / Drummond, J. / Frommlet, A. / Lu, C. / Franke, ...Authors: Davies, C.W. / Oh, A.J. / Mroue, R. / Steffek, M. / Bruning, J.M. / Xiao, Y. / Feng, S. / Jayakar, S. / Chan, E. / Arumugam, V. / Uribe, S.C. / Drummond, J. / Frommlet, A. / Lu, C. / Franke, Y. / Merchant, M. / Koeppen, H. / Quinn, J.G. / Malhotra, S. / Do, S. / Gazzard, L. / Purkey, H.E. / Rudolph, J. / Mulvihill, M.M. / Koerber, J.T. / Wang, W. / Evangelista, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.9 KB | Display | ![]() |
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PDB format | ![]() | 209.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 38.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mdpC ![]() 7rp2C ![]() 7rp4C ![]() 3r1gS ![]() 4dsuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19417.861 Da / Num. of mol.: 1 / Mutation: G12C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Antibody , 2 types, 2 molecules HI
#2: Antibody | Mass: 23833.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Antibody | Mass: 22878.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 7 types, 301 molecules ![](data/chem/img/MKZ.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MKZ / | ||||||
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#5: Chemical | ChemComp-GDP / | ||||||
#6: Chemical | ChemComp-MG / | ||||||
#7: Chemical | ChemComp-GOL / #8: Chemical | #9: Chemical | ChemComp-SO4 / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.91 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.10% n-Octyl-B-D-glucoside, 0.1 M sodium citrate pH 5.5, 22% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→45.36 Å / Num. obs: 83629 / % possible obs: 98.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 34.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Net I/σ(I): 15.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DSU, 3R1G Resolution: 2→33.577 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.86 / Phase error: 26.22 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.08 Å2 / Biso mean: 51.3508 Å2 / Biso min: 21.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→33.577 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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