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Open data
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Basic information
Entry | Database: PDB / ID: 5a2k | |||||||||
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Title | Crystal structure of scFv-SM3 in complex with APD-TGalNAc-RP | |||||||||
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![]() | IMMUNE SYSTEM / GLYCOPEPTIDES / ANTIBODIES / MOLECULAR RECOGNITION / CONFORMATION ANALYSIS / FUSION PROTEIN | |||||||||
Function / homology | ![]() immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / blood microparticle / immune response / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Martinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. ...Martinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. / Busto, J.H. / Bernardes, G.J.L. / Peregrina, J.M. / Hurtado-Guerrero, R. / Corzana, F. | |||||||||
![]() | ![]() Title: Deciphering the Non-Equivalence of Serine and Threonine O-Glycosylation Points: Implications for Molecular Recognition of the Tn Antigen by an Anti-Muc1 Antibody. Authors: Martinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. / Busto, J.H. / ...Authors: Martinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. / Busto, J.H. / Bernardes, G.J.L. / Peregrina, J.M. / Hurtado-Guerrero, R. / Corzana, 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 | ![]() | 105.9 KB | Display | ![]() |
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PDB format | ![]() | 80.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.8 KB | Display | ![]() |
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Full document | ![]() | 473.3 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a2iC ![]() 5a2jC ![]() 5a2lC ![]() 1sm3S 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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Unit cell |
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Components
#1: Antibody | Mass: 25742.338 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-115,20-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Protein/peptide | Mass: 656.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||
#3: Chemical | ChemComp-EDO / #4: Sugar | ChemComp-A2G / | #5: Water | ChemComp-HOH / | Sequence details | RESIDUE RANGE 1002-1107 FOR CHAIN H MAPS TO CHAIN L OF PDB ENTRY 1SM3 CHAIN P REPRESENTS A SHORTER ...RESIDUE RANGE 1002-1107 FOR CHAIN H MAPS TO CHAIN L OF PDB ENTRY 1SM3 CHAIN P REPRESENTS | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.01 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45 Å / Num. obs: 25092 / % possible obs: 100 % / Observed criterion σ(I): 1.8 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SM3 Resolution: 1.7→90.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.693 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.937 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→90.41 Å
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