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Yorodumi- PDB-6ypw: Crystal structure for the complex of human carbonic anhydrase II ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ypw | ||||||
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Title | Crystal structure for the complex of human carbonic anhydrase II and 4-((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)methoxy)benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Carbonic Anhydrase Inhibitors / AZT / Telomerase Inhibitors / Cancer / Molecular hybrids / Click Chemistry / Triazole. | ||||||
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 / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / 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: 1.1 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 | 6ypw.cif.gz | 133.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ypw.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ypw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ypw_validation.pdf.gz | 750.6 KB | Display | wwPDB validaton report |
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Full document | 6ypw_full_validation.pdf.gz | 752.8 KB | Display | |
Data in XML | 6ypw_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 6ypw_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/6ypw ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6ypw | HTTPS FTP |
-Related structure data
Related structure data | 7nh6C 3p58S 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 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-P75 / |
#4: 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: 41.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.2 M sodium citrate, 50 mM 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: Jul 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: 1.1→41.36 Å / Num. obs: 88794 / % possible obs: 90.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.1→1.11 Å / Num. unique obs: 2400 / CC1/2: 0.831 / % possible all: 49.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P58 Resolution: 1.1→41.09 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.661 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.11 Å2 / Biso mean: 12.45 Å2 / Biso min: 5.14 Å2
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Refinement step | Cycle: final / Resolution: 1.1→41.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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