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Open data
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Basic information
Entry | Database: PDB / ID: 7mdp | ||||||
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Title | KRas G12C in complex with G-2897 | ||||||
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![]() | HYDROLASE/Immune System / KRAS / GTPase / HYDROLASE / HYDROLASE-Immune System complex | ||||||
Function / homology | small monomeric GTPase / Ca2+ pathway / ACETATE ION / CACODYLIC ACID / GUANOSINE-5'-DIPHOSPHATE / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / 4-(trifluoromethyl)-1,3-benzothiazol-2-amine / Isoform 2B of GTPase KRas![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oh, A. / Frank, Y. / Wang, W. | ||||||
![]() | ![]() 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 | ![]() | 258.6 KB | Display | ![]() |
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PDB format | ![]() | 203.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 35.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rp2C ![]() 7rp3C ![]() 7rp4C ![]() 6xc8 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19317.850 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 , 9 types, 161 molecules ![](data/chem/img/Z07.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CAD.gif)
![](data/chem/img/P15.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CAD.gif)
![](data/chem/img/P15.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-Z07 / | ||||||||||
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#5: Chemical | ChemComp-GDP / | ||||||||||
#6: Chemical | ChemComp-MG / | ||||||||||
#7: Chemical | #8: Chemical | ChemComp-CAD / #9: Chemical | ChemComp-P15 / #10: Chemical | ChemComp-EDO / #11: Chemical | ChemComp-DMS / | #12: 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: 3.57 Å3/Da / Density % sol: 65.56 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH 6.0, 21 % PEG 4K and 0.2 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→37.902 Å / Num. obs: 75922 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 38.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.045 / Rrim(I) all: 0.083 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.07→2.18 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.64 / Num. measured all: 28439 / Num. unique obs: 8279 / CC1/2: 0.4 / Rpim(I) all: 1.043 / Rrim(I) all: 1.95 / Net I/σ(I) obs: 0.8 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6XC8 ![]() 6xc8 Resolution: 1.96→37.902 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 33.6 / 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: 164.64 Å2 / Biso mean: 57.5263 Å2 / Biso min: 19.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.96→37.902 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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