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Yorodumi- PDB-4knj: Crystal structure of human carbonic anhydrase isozyme II with 2-C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4knj | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme II with 2-Chloro-4-[(pyrimidin-2-ylsulfanyl)acetyl]benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / LYASE-LYASE INHIBITOR complex | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Smirnov, A. / Manakova, E. / Grazulis, S. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2013 Title: Benzenesulfonamides with pyrimidine moiety as inhibitors of human carbonic anhydrases I, II, VI, VII, XII, and XIII Authors: Capkauskaite, E. / Zubriene, A. / Smirnov, A. / Torresan, J. / Kisonaite, M. / Kazokaite, J. / Gylyte, J. / Michailoviene, V. / Jogaite, V. / Manakova, E. / Grazulis, S. / Tumkevicius, S. / Matulis, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4knj.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4knj.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 4knj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/4knj ftp://data.pdbj.org/pub/pdb/validation_reports/kn/4knj | HTTPS FTP |
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-Related structure data
Related structure data | 4kniC 4knmC 4knnC 4kp5C 4kp8C 3hljS 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 , 1 types, 1 molecules A
#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: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 160 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-E1F / |
#4: Chemical | ChemComp-DMS / |
#5: Chemical | ChemComp-MES / |
#6: 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: 39.7 % / Mosaicity: 0.9 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.2M sodium malonate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Nov 21, 2011 / Details: Detector swing-out angle up to 30 degrees | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.815 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→30.26 Å / Num. obs: 15098 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 21.207 Å2 / Rsym value: 0.11 / Net I/σ(I): 6.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HLJ Resolution: 2→30.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.844 / SU R Cruickshank DPI: 0.247 / SU Rfree: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.197 / 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 max: 46.83 Å2 / Biso mean: 18.888 Å2 / Biso min: 5.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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