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- PDB-7ued: Crystal structure of full length mesothelin bound with MORAb-009 Fab -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ued | ||||||
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Title | Crystal structure of full length mesothelin bound with MORAb-009 Fab | ||||||
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![]() | IMMUNE SYSTEM / Mesothelin | ||||||
Function / homology | ![]() Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell adhesion / endoplasmic reticulum lumen / Golgi apparatus / cell surface / extracellular region ...Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell adhesion / endoplasmic reticulum lumen / Golgi apparatus / cell surface / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhan, J. / Esser, L. / Lin, D. / Tang, W.K. / Xia, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of Cancer Antigen Mesothelin and Its Complexes with Therapeutic Antibodies. Authors: Zhan, J. / Lin, D. / Watson, N. / Esser, L. / Tang, W.K. / Zhang, A. / Liu, X. / Hassan, R. / Gleinich, A. / Shajahan, A. / Azadi, P. / Pastan, I. / Xia, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 497.4 KB | Display | ![]() |
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PDB format | ![]() | 345.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.5 KB | Display | ![]() |
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Full document | ![]() | 792.9 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u9jC ![]() 8cx3C ![]() 4f3fS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 23140.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#3: Antibody | Mass: 23246.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein / Sugars , 2 types, 2 molecules M
#1: Protein | Mass: 35261.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 36 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.81 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Tris, pH 7, 150 mM sodium citrate, 16.4% PEG3350, 100 mM lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 21609 / % possible obs: 85 % / Redundancy: 3.1 % / Biso Wilson estimate: 66.66 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 6.444 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.499 / Num. unique obs: 1755 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4F3F Resolution: 3→24.68 Å / SU ML: 0.3659 / Cross valid method: FREE R-VALUE / σ(F): 0.53 / Phase error: 22.7411 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 68.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→24.68 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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