+Open data
-Basic information
Entry | Database: PDB / ID: 6hx5 | ||||||
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Title | Selenols: a new class of Carbonic Anhydrase inhibitors | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | PROTEIN BINDING / inhibitor / carbonic anhydrase | ||||||
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 / Resolution: 1.44 Å | ||||||
Authors | Angeli, A. / Ferraroni, M. | ||||||
Citation | Journal: Chem. Commun. (Camb.) / Year: 2019 Title: Selenols: a new class of carbonic anhydrase inhibitors. Authors: Angeli, A. / Tanini, D. / Nocentini, A. / Capperucci, A. / Ferraroni, M. / Gratteri, P. / 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 | 6hx5.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hx5.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/6hx5 ftp://data.pdbj.org/pub/pdb/validation_reports/hx/6hx5 | 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
#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-GXE / |
#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: 41.29 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 8 / Details: 1.5 M sodium citrate, Tris 50 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→41 Å / Num. obs: 41176 / % possible obs: 98.1 % / Redundancy: 5.37 % / Net I/σ(I): 10.93 |
Reflection shell | Resolution: 1.44→1.58 Å |
-Processing
Software |
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Refinement | Resolution: 1.44→41 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.578 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.072 / 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: 14.848 Å2
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Refinement step | Cycle: 1 / Resolution: 1.44→41 Å
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Refine LS restraints |
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