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Yorodumi- PDB-5mjn: Three dimensional structure of human carbonic anhydrase II in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mjn | ||||||
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Title | Three dimensional structure of human carbonic anhydrase II in complex with 5-[(4Chlorobenzyl)sulfanyl]thiophene-2-sulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / CA2 / CA II / Carbonic Anhydrase 2 / Carbonic anhydrase II / sulfonamide | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å | ||||||
Authors | Leitans, J. / Tars, K. | ||||||
Citation | Journal: Bioorg. Med. Chem. / Year: 2017 Title: 5-Substituted-benzylsulfanyl-thiophene-2-sulfonamides with effective carbonic anhydrase inhibitory activity: Solution and crystallographic investigations. Authors: Ivanova, J. / Balode, A. / Zalubovskis, R. / Leitans, J. / Kazaks, A. / Vullo, D. / Tars, K. / 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 | 5mjn.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mjn.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/5mjn ftp://data.pdbj.org/pub/pdb/validation_reports/mj/5mjn | HTTPS FTP |
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-Related structure data
Related structure data | 4bf1S 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: 29157.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: PET / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-7O8 / |
#4: 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: 2.1 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 1,54 M SODIUM CITRATE 60 MM TRIS- HCL, PH 9.0, PROTEIN 10 MG/ML 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) VAPOR DIFFUSION, SITTING DROP, ...Details: 1,54 M SODIUM CITRATE 60 MM TRIS- HCL, PH 9.0, PROTEIN 10 MG/ML 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, TIME 2-5 DAYS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97671 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 26, 2013 / Details: MULTILAYER |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97671 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→18 Å / Num. obs: 81743 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 6.4 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.17→1.23 Å / Redundancy: 3 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.3 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BF1 Resolution: 1.17→18 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.037 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.697 Å2
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Refinement step | Cycle: 1 / Resolution: 1.17→18 Å
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Refine LS restraints |
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