+Open data
-Basic information
Entry | Database: PDB / ID: 3hku | ||||||
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Title | Human carbonic anhydrase II in complex with topiramate | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Carbonic anhydrase drug design / Acetylation / Cytoplasm / Disease mutation / Metal-binding / Polymorphism / Zinc | ||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Paul, B. / Poulsen, S.-A. / Hofmann, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: S-glycosyl primary sulfonamides--a new structural class for selective inhibition of cancer-associated carbonic anhydrases. Authors: Lopez, M. / Paul, B. / Hofmann, A. / Morizzi, J. / Wu, Q.K. / Charman, S.A. / Innocenti, A. / Vullo, D. / Supuran, C.T. / Poulsen, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hku.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hku.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/3hku ftp://data.pdbj.org/pub/pdb/validation_reports/hk/3hku | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET8c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-TOR / [( |
#4: 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: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 2.6M (NH4)2SO4, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 5, 2008 / Details: VariMax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→70.2 Å / Num. obs: 21463 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 13.634 Å2 / Rmerge(I) obs: 0.033 |
Reflection shell | Resolution: 1.8→1.848 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.058 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→70.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.259 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.122 / 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: 13.831 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→70.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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