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Open data
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Basic information
Entry | Database: PDB / ID: 3iet | |||||||||
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Title | Crystal Structure of 237mAb with antigen | |||||||||
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![]() | IMMUNE SYSTEM / glycopepitde / antibody / Fab / carbohydrate-biding / tumour | |||||||||
Function / homology | ![]() tube morphogenesis / regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / actin-mediated cell contraction / GPVI-mediated activation cascade / leading edge of lamellipodium / visceral serous pericardium development / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / lymphangiogenesis ...tube morphogenesis / regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / actin-mediated cell contraction / GPVI-mediated activation cascade / leading edge of lamellipodium / visceral serous pericardium development / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / lymphangiogenesis / regulation of lamellipodium morphogenesis / tetraspanin-enriched microdomain / positive regulation of platelet aggregation / filopodium membrane / wound healing, spreading of cells / anchoring junction / positive regulation of cell motility / prostaglandin metabolic process / lung alveolus development / microvillus membrane / regulation of G1/S transition of mitotic cell cycle / lamellipodium membrane / Rho protein signal transduction / lymph node development / positive regulation of epithelial to mesenchymal transition / regulation of cell adhesion / ruffle / filopodium / lung development / cell-cell adhesion / ruffle membrane / cell migration / lamellipodium / regulation of cell shape / cytoplasmic vesicle / basolateral plasma membrane / cell population proliferation / cell adhesion / positive regulation of cell migration / apical plasma membrane / membrane raft / signaling receptor binding / negative regulation of cell population proliferation / external side of plasma membrane / negative regulation of apoptotic process / signal transduction / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Brooks, C.L. / Evans, S.V. / Borisova, S.N. | |||||||||
![]() | ![]() Title: Antibody recognition of a unique tumor-specific glycopeptide antigen. Authors: Brooks, C.L. / Schietinger, A. / Borisova, S.N. / Kufer, P. / Okon, M. / Hirama, T. / Mackenzie, C.R. / Wang, L.X. / Schreiber, H. / Evans, S.V. #1: ![]() Title: A mutant chaperone converts a wild-type protein into a tumor-specific antien Authors: Schietinger, A. / Philip, M. / Yoshida, B.A. / Azadi, P. / Liu, H. / Meredith, S.C. / Schreiber, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.4 KB | Display | ![]() |
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PDB format | ![]() | 150.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.2 KB | Display | ![]() |
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Full document | ![]() | 486.8 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3if1C ![]() 1m71S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 4 molecules ACBD
#1: Antibody | Mass: 23823.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 23538.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Protein/peptide / Sugars , 2 types, 4 molecules XQ

#3: Protein/peptide | Mass: 984.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #5: Sugar | |
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-Non-polymers , 2 types, 525 molecules 


#4: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG MME 5000, ZnCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 13, 2007 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→19.86 Å / Num. obs: 48616 / % possible obs: 98.5 % / Redundancy: 7.96 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1M71 Resolution: 2.2→19.86 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.88 / σ(F): 1.34 / Phase error: 28.59 / 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 / Bsol: 61.301 Å2 / ksol: 0.377 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.633 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.86 Å
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Refine LS restraints |
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LS refinement shell |
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