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Yorodumi- PDB-7bhh: 4-(2-(3-(4-iodophenyl)selenoureido)ethyl)benzenesulfonamide in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bhh | ||||||
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Title | 4-(2-(3-(4-iodophenyl)selenoureido)ethyl)benzenesulfonamide in complex with Carbonic Anhydrase II | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / carbonic anhydrase / inibitor / sulfonamide / organoseleno | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.4 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 | 7bhh.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bhh.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 7bhh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bhh_validation.pdf.gz | 709.2 KB | Display | wwPDB validaton report |
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Full document | 7bhh_full_validation.pdf.gz | 709.5 KB | Display | |
Data in XML | 7bhh_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 7bhh_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/7bhh ftp://data.pdbj.org/pub/pdb/validation_reports/bh/7bhh | HTTPS FTP |
-Related structure data
Related structure data | 6qqmC 7bfaC 7bg5C 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-TN8 / ~{ |
#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: 41.1 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5-1.7 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 PILATUS3 S 6M / Detector: PIXEL / Date: Sep 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→41.05 Å / Num. obs: 92147 / % possible obs: 98.7 % / Redundancy: 3.189 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.043 / Rsym value: 0.035 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.4→1.49 Å / Rmerge(I) obs: 0.391 / Num. unique obs: 14333 / CC1/2: 0.814 / Rrim(I) all: 0.484 / Rsym value: 0.424 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FIK Resolution: 1.4→41.05 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.931 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 223.05 Å2 / Biso mean: 17.6 Å2 / Biso min: 8.55 Å2
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Refinement step | Cycle: final / Resolution: 1.4→41.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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