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Yorodumi- PDB-3k7k: Crystal structure of the complex between Carbonic Anhydrase II an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k7k | ||||||
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Title | Crystal structure of the complex between Carbonic Anhydrase II and anions | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Inorganic anion / Trithiocarbonate / x ray / carbonic anhydrase II | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Temperini, C. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Carbonic anhydrase inhibitors. X-ray crystal studies of the carbonic anhydrase II-trithiocarbonate adduct-An inhibitor mimicking the sulfonamide and urea binding to the enzyme Authors: Temperini, C. / Scozzafava, A. / 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 | 3k7k.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k7k.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 3k7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/3k7k ftp://data.pdbj.org/pub/pdb/validation_reports/k7/3k7k | HTTPS FTP |
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-Related structure data
Related structure data | 1ca2S 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
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: The protein was purchased from Sigma-aldrich. / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-HG / |
#4: Chemical | ChemComp-KCS / |
#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: 2.08 Å3/Da / Density % sol: 40.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: Tris.HCl pH 7.7-7.8 , sodium 4-(hydroxymercury)benzoate , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å |
Detector | Type: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Feb 2, 2009 |
Radiation | Monochromator: capillary / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→10.35 Å / Num. all: 39228 / Num. obs: 37400 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.17 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 7480 / Rsym value: 0.38 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CA2 Resolution: 1.9→10.35 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.897 / SU B: 3.838 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.171 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.795 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→10.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.948 Å / Total num. of bins used: 20
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