+Open data
-Basic information
Entry | Database: PDB / ID: 5fv9 | ||||||
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Title | Crystal structure of GalNAc-T2 in complex with compound 16d | ||||||
Components | GALNAC-T2 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / Golgi cisterna membrane ...protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / Golgi cisterna membrane / protein maturation / manganese ion binding / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular region / membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Ghirardello, M. / Rivas, M. / Lacetera, A. / Delso, I. / Lira-Navarrete, E. / Tejero, T. / Martin-Santamaria, S. / Hurtado-Guerrero, R. / Merino, P. | ||||||
Citation | Journal: Chemistry / Year: 2016 Title: Glycomimetics Targeting Glycosyltransferases: Synthetic, Computational and Structural Studies of Less-Polar Conjugates. Authors: Ghirardello, M. / De Las Rivas, M. / Lacetera, A. / Delso, I. / Lira-Navarrete, E. / Tejero, T. / Martin-Santamaria, S. / Hurtado-Guerrero, R. / Merino, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fv9.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5fv9.ent.gz | 985.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fv9_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 5fv9_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 5fv9_validation.xml.gz | 131.3 KB | Display | |
Data in CIF | 5fv9_validation.cif.gz | 180.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/5fv9 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/5fv9 | HTTPS FTP |
-Related structure data
Related structure data | 4dotS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.05266, 0.9073, -0.4171), Vector: |
-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 64824.703 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZALPHAA / Production host: KOMAGATAELLA PASTORIS (fungus) / Variant (production host): X33 / References: UniProt: Q10471 |
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-Non-polymers , 6 types, 1667 molecules
#2: Chemical | ChemComp-UDP / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.06 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→20 Å / Num. obs: 215817 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.07→2.12 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4DOT Resolution: 2.07→250.15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 10.755 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.178 / 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: 48.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→250.15 Å
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