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Yorodumi- PDB-6wka: human carbonic anhydrase II bound to an inhibitor modified with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wka | ||||||
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Title | human carbonic anhydrase II bound to an inhibitor modified with azidothymidine | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / human CA II / inhibitor / click chemistry / azidothymidine | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Peat, T.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Azidothymidine "Clicked" into 1,2,3-Triazoles: First Report on Carbonic Anhydrase-Telomerase Dual-Hybrid Inhibitors. Authors: Berrino, E. / Angeli, A. / Zhdanov, D.D. / Kiryukhina, A.P. / Milaneschi, A. / De Luca, A. / Bozdag, M. / Carradori, S. / Selleri, S. / Bartolucci, G. / Peat, T.S. / Ferraroni, M. / Supuran, C.T. / Carta, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wka.cif.gz | 133.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wka.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wka ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wka | HTTPS FTP |
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-Related structure data
Related structure data | 5fltS S: Starting model for refinement |
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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-U4V / |
#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: 41.06 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 7.5 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→41.52 Å / Num. obs: 51588 / % possible obs: 95 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.031 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.34→1.36 Å / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1978 / CC1/2: 0.848 / Rpim(I) all: 0.208 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5flt Resolution: 1.34→39.875 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.827 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.053 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.385 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→39.875 Å
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Refine LS restraints |
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LS refinement shell |
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