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Open data
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Basic information
Entry | Database: PDB / ID: 8fsl | ||||||
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Title | Human Mesothelin bound to a neutralizing VH domain antibody | ||||||
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![]() | ANTITUMOR PROTEIN / Mesothelin VH | ||||||
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 | ![]() ![]() Insect expression vector pBlueBacmsGCA1His (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Calero, G. | ||||||
Funding support | 1items
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![]() | ![]() Title: Preclinical assessment of a novel human antibody VH domain targeting mesothelin as an antibody-drug conjugate. Authors: Sun, Z. / Chu, X. / Adams, C. / Ilina, T.V. / Guerrero, M. / Lin, G. / Chen, C. / Jelev, D. / Ishima, R. / Li, W. / Mellors, J.W. / Calero, G. / Dimitrov, D.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 400.7 KB | Display | ![]() |
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PDB format | ![]() | 332.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.8 KB | Display | ![]() |
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Full document | ![]() | 517.2 KB | Display | |
Data in XML | ![]() | 37.9 KB | Display | |
Data in CIF | ![]() | 51.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 12806.857 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 32167.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Insect expression vector pBlueBacmsGCA1His (others) Gene: MSLN, MPF Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q13421 Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 75 % / Description: 40% |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / Details: PEG3350 20% 0.15 M ammonium nitrate |
-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: Jul 31, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98008 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→114 Å / Num. obs: 51008 / % possible obs: 99 % / Redundancy: 109 % / Biso Wilson estimate: 101.44 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.055 / Rrim(I) all: 0.384 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.9→2.99 Å / Redundancy: 110 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 111 / Num. unique obs: 4354 / CC1/2: 0.21 / Rpim(I) all: 0.47 / Rrim(I) all: 0.36 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→39.9 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -51.4914 Å / Origin y: -26.0968 Å / Origin z: 26.3841 Å
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Refinement TLS group | Selection details: all |