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Open data
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Basic information
Entry | Database: PDB / ID: 6ug7 | |||||||||
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Title | Complex of ch28/11 Fab and SSEA-4 (tetragonal form) | |||||||||
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![]() | IMMUNE SYSTEM / IMMUNOGLOBULIN / CHIMERIC ANTIBODY / ANTIGEN BINDING FRAGMENT / SSEA-4 / COMPLEX | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Soliman, C. / Ramsland, P.A. | |||||||||
![]() | ![]() Title: The terminal sialic acid of stage-specific embryonic antigen-4 has a crucial role in binding to a cancer-targeting antibody. Authors: Soliman, C. / Chua, J.X. / Vankemmelbeke, M. / McIntosh, R.S. / Guy, A.J. / Spendlove, I. / Durrant, L.G. / Ramsland, P.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.3 KB | Display | ![]() |
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PDB format | ![]() | 85.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 880.9 KB | Display | ![]() |
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Full document | ![]() | 882.5 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 38 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ug8C ![]() 6ug9C ![]() 6ugaC ![]() 1a7nS ![]() 3iu4S 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
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23166.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 23016.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 1 types, 1 molecules
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 603 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-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 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 4000, sodium acetate, ammonium 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: Apr 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. obs: 84916 / % possible obs: 99.9 % / Redundancy: 13.3 % / Rrim(I) all: 0.1 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.5→1.6 Å / Num. unique obs: 13419 / Rrim(I) all: 0.48 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A7N, 3IU4 Resolution: 1.52→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.72 Å2 / Biso mean: 25.4528 Å2 / Biso min: 9.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.56 Å / Total num. of bins used: 20
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