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Yorodumi- PDB-3r16: Human CAII bound to N-(4-sulfamoylphenyl)-2-(thiophen-2-yl) acetamide -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r16 | ||||||
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Title | Human CAII bound to N-(4-sulfamoylphenyl)-2-(thiophen-2-yl) acetamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / reversible hydration of carbondioxide | ||||||
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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Biswas, S. / McKenna, R. / Supuran, C.T. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2011 Title: Conformational variability of different sulfonamide inhibitors with thienyl-acetamido moieties attributes to differential binding in the active site of cytosolic human carbonic anhydrase isoforms. Authors: Biswas, S. / Aggarwal, M. / Guzel, O. / Scozzafava, A. / McKenna, R. / Supuran, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r16.cif.gz | 76.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r16.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 3r16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/3r16 ftp://data.pdbj.org/pub/pdb/validation_reports/r1/3r16 | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28932.641 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) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 332 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-5UN / | #5: Chemical | ChemComp-DMS / | #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: 2.12 Å3/Da / Density % sol: 41.96 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.8 Details: 1.6M sodium citrate, tris buffer, pH 7.8, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 22, 2011 |
Radiation | Monochromator: varimax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 29653 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.88 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 20.78 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.069 / Mean I/σ(I) obs: 4.9 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→25.404 Å / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.9111 / SU ML: 0.17 / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.313 Å2 / ksol: 0.385 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.4 Å2 / Biso mean: 16.0762 Å2 / Biso min: 5.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→25.404 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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