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Open data
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Basic information
Entry | Database: PDB / ID: 9fy8 | |||||||||
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Title | L2A5 Fab in complex with STn-Thr | |||||||||
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![]() | SUGAR BINDING PROTEIN / Antibody / Fab / Immune system | |||||||||
Function / homology | : / THREONINE![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Laugieri, M.E. / Ereno Orbea, J. / Jimenez Barbero, J. / Oyenarte, I. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Decoding the Molecular Basis of the Specificity of an Anti-sTn Antibody. Authors: Soares, C.O. / Laugieri, M.E. / Grosso, A.S. / Natale, M. / Coelho, H. / Behren, S. / Yu, J. / Cai, H. / Franconetti, A. / Oyenarte, I. / Magnasco, M. / Gimeno, A. / Ramos, N. / Chai, W. / ...Authors: Soares, C.O. / Laugieri, M.E. / Grosso, A.S. / Natale, M. / Coelho, H. / Behren, S. / Yu, J. / Cai, H. / Franconetti, A. / Oyenarte, I. / Magnasco, M. / Gimeno, A. / Ramos, N. / Chai, W. / Corzana, F. / Westerlind, U. / Jimenez-Barbero, J. / Palma, A.S. / Videira, P.A. / Ereno-Orbea, J. / Marcelo, F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.6 KB | Display | ![]() |
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PDB format | ![]() | 165.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 605.6 KB | Display | ![]() |
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Full document | ![]() | 611.8 KB | Display | |
Data in XML | ![]() | 41.8 KB | Display | |
Data in CIF | ![]() | 56.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9fxtC 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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2 | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 4 molecules BICL
#1: Antibody | Mass: 23231.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 23313.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein / Sugars , 2 types, 4 molecules DV
#3: Protein | Mass: 12070.028 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Polysaccharide | Source method: isolated from a genetically manipulated source Details: Sialyl-Tn (sTn) antigen is a truncated O-glycan containing a sialic acid alpha-2,6 linked to N-acetylgalactosamine (GalNAc) alpha-O-threonine or to N-acetylgalactosamine (GalNAc) alpha-O-serine. References: BIRD: PRD_002574 |
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-Non-polymers , 2 types, 141 molecules 


#5: Chemical | ![]() Details: Sialyl-Tn (sTn) antigen is a truncated O-glycan containing a sialic acid alpha-2,6 linked to N-acetylgalactosamine (GalNAc) alpha-O-threonine or to N-acetylgalactosamine (GalNAc) alpha-O-serine. References: BIRD: PRD_002574 #6: Water | ChemComp-HOH / | |
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-Details
Compound details | Activation of an aberrant glycosylation pathway in cancer cells can lead to expression of the onco- ...Activation of an aberrant glycosylation pathway in cancer cells can lead to expression of the onco-foetal sialyl-Tn (sTn) antigen. |
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Has ligand of interest | Y |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 0.1M BisTris:Hcl, pH6.5, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 30, 2023 | ||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection | Resolution: 2.62→97.892 Å / Num. obs: 34129 / % possible obs: 97.6 % / Redundancy: 5.13 % / CC1/2: 0.961 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.302 / Net I/σ(I): 4.5 | ||||||||||||||||||||
Reflection shell |
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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: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→53.61 Å
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Refine LS restraints |
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LS refinement shell |
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