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- PDB-4kni: Crystal structure of human carbonic anhydrase isozyme II with 2-C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kni | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme II with 2-Chloro-4-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 / morphogenesis of an epithelium / regulation of intracellular pH / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Smirnov, A. / Manakova, E. / Grazulis, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.1 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.6 KB | Display | ![]() |
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Full document | ![]() | 759.9 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4knjC ![]() 4knmC ![]() 4knnC ![]() 4kp5C ![]() 4kp8C ![]() 3hljS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 195 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/E1E.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/E1E.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-MES / | #5: Chemical | ChemComp-E1E / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40.4 % / Mosaicity: 0.6 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M sodium BICINE pH 9, 0.2M ammonium sulfate, 2M sodium malonate pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 5, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: VARIMAX-HF MIRROR / 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→17.637 Å / Num. obs: 20965 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 18.188 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 19.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3HLJ Resolution: 1.8→17.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.863 / SU R Cruickshank DPI: 0.155 / SU Rfree: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.47 Å2 / Biso mean: 17.14 Å2 / Biso min: 3.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→17.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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