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Yorodumi- PDB-7nh6: Crystal structure of human carbonic anhydrase II with 3-(3-((1-(2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nh6 | ||||||
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Title | Crystal structure of human carbonic anhydrase II with 3-(3-((1-(2-(hydroxymethyl)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-3-yl)-1H-1,2,3-triazol-4-yl)methyl)ureido)benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / carbonic anhydrase II / inhibitor / metalloenzyme / 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 / 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: 1.28 Å | ||||||
Authors | Angeli, A. / Ferraroni, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Mechanisms of the Antiproliferative and Antitumor Activity of Novel Telomerase-Carbonic Anhydrase Dual-Hybrid Inhibitors. Authors: Plyasova, A.A. / Berrino, E. / Khan, I.I. / Veselovsky, A.V. / Pokrovsky, V.S. / Angeli, A. / Ferraroni, M. / Supuran, C.T. / Pokrovskaya, M.V. / Alexandrova, S.S. / Gladilina, Y.A. / ...Authors: Plyasova, A.A. / Berrino, E. / Khan, I.I. / Veselovsky, A.V. / Pokrovsky, V.S. / Angeli, A. / Ferraroni, M. / Supuran, C.T. / Pokrovskaya, M.V. / Alexandrova, S.S. / Gladilina, Y.A. / Sokolov, N.N. / Hilal, A. / Carta, F. / Zhdanov, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nh6.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nh6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nh6_validation.pdf.gz | 764.6 KB | Display | wwPDB validaton report |
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Full document | 7nh6_full_validation.pdf.gz | 766.3 KB | Display | |
Data in XML | 7nh6_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 7nh6_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/7nh6 ftp://data.pdbj.org/pub/pdb/validation_reports/nh/7nh6 | HTTPS FTP |
-Related structure data
Related structure data | 6ypwC 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-UDE / |
#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: 2.08 Å3/Da / Density % sol: 40.89 % |
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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: 1.0001 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0001 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→41.2 Å / Num. obs: 62015 / % possible obs: 99.7 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.021 / Rrim(I) all: 0.039 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.28→1.3 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 2964 / CC1/2: 0.972 / Rpim(I) all: 0.139 / Rrim(I) all: 0.217 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FIK Resolution: 1.28→39.966 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.58 / SU ML: 0.026 / Cross valid method: NONE / ESU R: 0.044 / ESU R Free: 0.046 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: 14.394 Å2
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Refinement step | Cycle: LAST / Resolution: 1.28→39.966 Å
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Refine LS restraints |
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LS refinement shell |
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