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- PDB-5ajo: Crystal structure of the inactive form of GalNAc-T2 in complex wi... -
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Basic information
Entry | Database: PDB / ID: 5ajo | |||||||||
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Title | Crystal structure of the inactive form of GalNAc-T2 in complex with the glycopeptide MUC5AC-3,13 | |||||||||
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![]() | TRANSFERASE / AFM / SAXS / LECTIN DOMAIN / COARSE-GRAINED MODEL / GLYCOPEPTIDES / INACTIVE FORM / ACTIVE FORM / COMPACT FORM / EXTENDED FORM | |||||||||
Function / homology | ![]() mucus layer / protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-glycan processing ...mucus layer / protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / extracellular matrix structural constituent / Golgi cisterna membrane / Dectin-2 family / protein maturation / extracellular matrix / Golgi lumen / manganese ion binding / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lira-Navarrete, E. / delasRivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. ...Lira-Navarrete, E. / delasRivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / Clausen, H. / Lostao, A. / Corzana, F. / Hurtado-Guerrero, R. | |||||||||
![]() | ![]() Title: Dynamic Interplay between Catalytic and Lectin Domains of Galnac-Transferases Modulates Protein O-Glycosylation. Authors: Lira-Navarrete, E. / De Las Rivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / ...Authors: Lira-Navarrete, E. / De Las Rivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / Clausen, H. / Lostao, A. / Corzana, F. / Hurtado-Guerrero, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.1 KB | Display | ![]() |
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PDB format | ![]() | 186.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.4 KB | Display | ![]() |
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Full document | ![]() | 488.9 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 47.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ajnC ![]() 5ajpC ![]() 4d0tS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 64824.703 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase | ||||
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#2: Protein/peptide | Mass: 1546.632 Da / Num. of mol.: 1 / Fragment: RESIDUES 65-79 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
#3: Sugar | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.04 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→20 Å / Num. obs: 110205 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.48→1.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.3 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4D0T Resolution: 1.48→89.54 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.135 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / 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: 21.137 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→89.54 Å
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Refine LS restraints |
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