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Yorodumi- PDB-2yhy: Structure of N-Acetylmannosamine kinase in complex with N- acetyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yhy | ||||||
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Title | Structure of N-Acetylmannosamine kinase in complex with N- acetylmannosamine and ADP | ||||||
Components | BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE | ||||||
Keywords | TRANSFERASE / SUGAR KINASE / SIALIC ACID / ROK FAMILY | ||||||
Function / homology | Function and homology information Defective GNE causes sialuria, NK and IBM2 / UDP-N-acetylglucosamine 2-epimerase (hydrolysing) / N-acetylglucosamine biosynthetic process / N-acylmannosamine kinase / N-acylmannosamine kinase activity / N-acetylneuraminate biosynthetic process / hexokinase activity / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine metabolic process / Sialic acid metabolism ...Defective GNE causes sialuria, NK and IBM2 / UDP-N-acetylglucosamine 2-epimerase (hydrolysing) / N-acetylglucosamine biosynthetic process / N-acylmannosamine kinase / N-acylmannosamine kinase activity / N-acetylneuraminate biosynthetic process / hexokinase activity / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine metabolic process / Sialic acid metabolism / hydrolase activity, hydrolyzing O-glycosyl compounds / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Martinez, J. / Nguyen, L.D. / Tauberger, E. / Hinderlich, S. / Reutter, W. / Fan, H. / Saenger, W. / Moniot, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Crystal Structures of N-Acetylmannosamine Kinase Provide Insights Into Enzyme Specificity and Inhibition Authors: Martinez, J. / Nguyen, L.D. / Tauberger, E. / Hinderlich, S. / Reutter, W. / Fan, H. / Saenger, W. / Moniot, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yhy.cif.gz | 145.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yhy.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yhy_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2yhy_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2yhy_validation.xml.gz | 18 KB | Display | |
Data in CIF | 2yhy_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/2yhy ftp://data.pdbj.org/pub/pdb/validation_reports/yh/2yhy | HTTPS FTP |
-Related structure data
Related structure data | 2yhwC 2yi1C 3eo3S C: citing same article (ref.) 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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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 36639.016 Da / Num. of mol.: 1 Fragment: N-ACETYLMANNOSAMINE KINASE DOMAIN, RESIDUES 406-720 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A-MNK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9Y223, N-acylmannosamine kinase |
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#2: Sugar | ChemComp-BM3 / |
-Non-polymers , 10 types, 211 molecules
#3: Chemical | ChemComp-CA / | ||||||||||||
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#4: Chemical | ChemComp-2PE / | ||||||||||||
#5: Chemical | ChemComp-PG4 / | ||||||||||||
#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-MG / | #9: Chemical | ChemComp-ADP / | #10: Chemical | ChemComp-CL / | #11: Chemical | ChemComp-ZN / | #12: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.37 % / Description: NONE |
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Crystal grow | Details: 0.2 M CALCIUM ACETATE, 0.1M SODIUM CACODYLATE PH 6.5, 40% PEG 300. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.981 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.981 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 489925 / % possible obs: 100 % / Observed criterion σ(I): 4.4 / Redundancy: 12.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.07 |
Reflection shell | Resolution: 1.82→1.92 Å / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EO3 Resolution: 1.82→41.26 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.37 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.092 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.605 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→41.26 Å
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