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Yorodumi- PDB-4kuv: Crystal structure of human carbonic anhydrase II in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kuv | ||||||
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Title | Crystal structure of human carbonic anhydrase II in complex with the 5-(3-(4-chlorophenylsulfonyl)ureido)pyridine-2-sulfonamide inhibitor | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE inhibitor / LYASE / 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 / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / 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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 Å | ||||||
Authors | Ferraroni, M. | ||||||
Citation | Journal: to be published Title: New classes of carbonic anhydrase inhibitors Authors: Ferraroni, M. / Supuran, C.T. / Carta, F. / Bozdag, M. / Scozzafava, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kuv.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kuv.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 4kuv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kuv_validation.pdf.gz | 746.8 KB | Display | wwPDB validaton report |
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Full document | 4kuv_full_validation.pdf.gz | 748.4 KB | Display | |
Data in XML | 4kuv_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 4kuv_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/4kuv ftp://data.pdbj.org/pub/pdb/validation_reports/ku/4kuv | HTTPS FTP |
-Related structure data
Related structure data | 4kuwC 4kuyC 4rh2C 4wl4C 3p58S 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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Details | monomer |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28794.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 265 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-MB6 / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-BME / |
#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: 2.13 Å3/Da / Density % sol: 42.15 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 8 Details: 1.5 M sodium citrate, Tris 50 mM, pH 8.0, VAPOR DIFFUSION, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.19→71.3815 Å / Num. obs: 55094 / % possible obs: 71.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.539 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.42 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3P58 Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1764 / WRfactor Rwork: 0.1563 / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.9216 / SU B: 0.649 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0536 / SU Rfree: 0.0544 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.054 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.94 Å2 / Biso mean: 11.8563 Å2 / Biso min: 3.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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