+Open data
-Basic information
Entry | Database: PDB / ID: 5cxy | |||||||||
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Title | Structure of a Glycosyltransferase in Complex with Inhibitor | |||||||||
Components | Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase | |||||||||
Keywords | Transferase/Transferase Inhibitor / sialyltransferase / inhibitor / polysialyltransferase / Transferase-Transferase Inhibitor complex | |||||||||
Function / homology | Function and homology information alpha-N-acetylneuraminate alpha-2,8-sialyltransferase / Transferases; Glycosyltransferases; Sialyltransferases / ganglioside biosynthetic process / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / sialylation / glycosphingolipid biosynthetic process / N-Glycan antennae elongation / glycoprotein metabolic process / Sialic acid metabolism / sialic acid binding ...alpha-N-acetylneuraminate alpha-2,8-sialyltransferase / Transferases; Glycosyltransferases; Sialyltransferases / ganglioside biosynthetic process / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / sialylation / glycosphingolipid biosynthetic process / N-Glycan antennae elongation / glycoprotein metabolic process / Sialic acid metabolism / sialic acid binding / oligosaccharide metabolic process / N-glycan processing / protein glycosylation / Golgi membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Volkers, G. / Strynadka, N.C.J. | |||||||||
Citation | Journal: To be published Title: To be published. Authors: Volkers, G. / Strynadka, N.C.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cxy.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cxy.ent.gz | 112.2 KB | Display | PDB format |
PDBx/mmJSON format | 5cxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/5cxy ftp://data.pdbj.org/pub/pdb/validation_reports/cx/5cxy | HTTPS FTP |
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-Related structure data
Related structure data | 5bo6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 89 - 380 / Label seq-ID: 32 - 323
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37919.012 Da / Num. of mol.: 2 / Fragment: UNP residues 81-380 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ST8SIA3, SIAT8C / Plasmid: pFHMSP LIC N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: O43173, EC: 2.4.99.- |
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-Sugars , 4 types, 8 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | |
-Non-polymers , 2 types, 137 molecules
#5: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 61.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 130 mM (NH)4H2PO4, 22% PEG2000 and 50 mM PIPES pH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.502 Å | |||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.502 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.15→52.72 Å / Num. obs: 48673 / % possible obs: 100 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.047 / Net I/σ(I): 11.8 / Num. measured all: 200266 / Scaling rejects: 47 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BO6 Resolution: 2.15→52.72 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.279 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.57 Å2 / Biso mean: 38.139 Å2 / Biso min: 16.39 Å2
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Refinement step | Cycle: final / Resolution: 2.15→52.72 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 33152 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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