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- PDB-6zl5: CRYSTAL STRUCTURE OF KRAS-G12D(C118S) IN COMPLEX WITH BI-2852 AND GDP -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zl5 | ||||||
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Title | CRYSTAL STRUCTURE OF KRAS-G12D(C118S) IN COMPLEX WITH BI-2852 AND GDP | ||||||
![]() | GTPase KRas | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() forebrain astrocyte development / negative regulation of epithelial cell differentiation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kessler, D. / Fischer, G. / Boettcher, J. | ||||||
![]() | ![]() Title: Drugging all RAS isoforms with one pocket. Authors: Kessler, D. / Bergner, A. / Bottcher, J. / Fischer, G. / Dobel, S. / Hinkel, M. / Mullauer, B. / Weiss-Puxbaum, A. / McConnell, D.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.6 KB | Display | ![]() |
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PDB format | ![]() | 63.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zioC ![]() 6zirC ![]() 6zizC ![]() 6zj0C ![]() 6zl3C ![]() 6zliC ![]() 6gj8S 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: 19370.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 187 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/F0K.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/F0K.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-GDP / ![]() |
#4: Chemical | ChemComp-F0K / ( |
#5: Chemical | ChemComp-SO4 / ![]() |
#6: 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: 4.13 Å3/Da / Density % sol: 70.25 % |
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Crystal grow![]() | Temperature: 278 K / Method: vapor diffusion Details: 2M Ammonium sulfate 100mM Sodium cacodylate 200mM Sodium cloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.765→60.49 Å / Num. obs: 28821 / % possible obs: 92.3 % / Redundancy: 17 % / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.765→1.771 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.158 / Mean I/σ(I) obs: 2 / Num. unique obs: 945 / Rsym value: 1.158 / % possible all: 60.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6GJ8 Resolution: 1.645→60.49 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.087 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.094 / SU Rfree Blow DPI: 0.087 / SU Rfree Cruickshank DPI: 0.083
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Displacement parameters | Biso mean: 17.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.645→60.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.7 Å /
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Refinement TLS params. | Origin x: -30.403 Å / Origin y: 12.1909 Å / Origin z: 9.3218 Å
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Refinement TLS group | Selection details: { A|* } |