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Yorodumi- PDB-7bg5: 4-(2-(3-(4-iodophenyl)ureido)ethyl)benzenesulfonamide in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bg5 | ||||||
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Title | 4-(2-(3-(4-iodophenyl)ureido)ethyl)benzenesulfonamide in complex with Carbonic Anhydrase II | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / carbonic anhydrase II / inhibitor / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.428 Å | ||||||
Authors | Angeli, A. / Ferraroni, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structural Insights into Schistosoma mansoni Carbonic Anhydrase (SmCA) Inhibition by Selenoureido-Substituted Benzenesulfonamides. Authors: Angeli, A. / Ferraroni, M. / Da'dara, A.A. / Selleri, S. / Pinteala, M. / Carta, F. / Skelly, P.J. / 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 | 7bg5.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bg5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7bg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bg5_validation.pdf.gz | 636.8 KB | Display | wwPDB validaton report |
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Full document | 7bg5_full_validation.pdf.gz | 637.8 KB | Display | |
Data in XML | 7bg5_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 7bg5_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/7bg5 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/7bg5 | HTTPS FTP |
-Related structure data
Related structure data | 6qqmC 7bfaC 7bhhC 7bm4C 7nexC 7ng1C 7nwyC 7o2sC 7o48C 7oa1C 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) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-TKQ / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 41.25 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 1.5 M sodium citrate, 0.1 M Tris pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.428→35.7 Å / Num. obs: 87572 / % possible obs: 99.2 % / Redundancy: 3.23 % / CC1/2: 0.99 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.042 / Rsym value: 0.038 / Net I/σ(I): 20.14 |
Reflection shell | Resolution: 1.428→1.51 Å / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 8.18 / Num. unique obs: 14196 / CC1/2: 0.985 / Rrim(I) all: 0.122 / Rsym value: 0.136 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FIK Resolution: 1.428→35.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.768 / SU ML: 0.031 / Cross valid method: NONE / ESU R: 0.056 / ESU R Free: 0.056 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.842 Å2
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Refinement step | Cycle: LAST / Resolution: 1.428→35.7 Å
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Refine LS restraints |
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LS refinement shell |
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