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Yorodumi- PDB-4rh2: Crystal structure of human carbonic anhydrase II in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rh2 | ||||||
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Title | Crystal structure of human carbonic anhydrase II in complex with 2-(6-hydroxy-3-Oxo-3H-xanthen-9-yl)-5-{3-1-(4-sulfamoyl-phenyl)-1h-[1,2,3]triazol-4-ylmethyl-thioureido}-benzoic acid | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 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 | 4rh2.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rh2.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 4rh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rh2_validation.pdf.gz | 686.3 KB | Display | wwPDB validaton report |
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Full document | 4rh2_full_validation.pdf.gz | 690 KB | Display | |
Data in XML | 4rh2_validation.xml.gz | 17 KB | Display | |
Data in CIF | 4rh2_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/4rh2 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/4rh2 | HTTPS FTP |
-Related structure data
Related structure data | 4kuvC 4kuwC 4kuyC 4wl4C 4fikS S: Starting model for refinement C: citing same article (ref.) |
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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
#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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-FC9 / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.09 Å3/Da / Density % sol: 41.06 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 8 Details: 1.6 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: Dec 10, 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: 1.3→30 Å / Num. all: 50556 / Num. obs: 50556 / % possible obs: 84.7 % / Observed criterion σ(I): -3 / Redundancy: 2.07 % / Biso Wilson estimate: 15.639 Å2 / Rmerge(I) obs: 0.022 / Χ2: 0.991 / Net I/σ(I): 23.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4FIK Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.1684 / FOM work R set: 0.9069 / SU B: 0.645 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0574 / SU Rfree: 0.0558 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 61.54 Å2 / Biso mean: 13 Å2 / Biso min: 4.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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