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Yorodumi- PDB-6qn2: Three dimensional structure of human carbonic anhydrase IX in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qn2 | ||||||
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Title | Three dimensional structure of human carbonic anhydrase IX in complex with benzenesulfonamide | ||||||
Components | Carbonic anhydrase 9 | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / Reversible hydration of carbon dioxide / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process ...Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / Reversible hydration of carbon dioxide / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / basolateral plasma membrane / response to hypoxia / response to xenobiotic stimulus / nucleolus / zinc ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Leitans, J. / Tars, K. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2020 Title: Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms. Authors: Zaksauskas, A. / Capkauskaite, E. / Jezepcikas, L. / Linkuviene, V. / Paketuryte, V. / Smirnov, A. / Leitans, J. / Kazaks, A. / Dvinskis, E. / Manakova, E. / Grazulis, S. / Tars, K. / Matulis, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qn2.cif.gz | 222.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qn2.ent.gz | 176.6 KB | Display | PDB format |
PDBx/mmJSON format | 6qn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/6qn2 ftp://data.pdbj.org/pub/pdb/validation_reports/qn/6qn2 | HTTPS FTP |
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-Related structure data
Related structure data | 6qn0C 6qn5C 6qn6C 6qnlC 6qutC 6r6fC 6r6jC 6r6yC 6r71C 6fe2S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28172.684 Da / Num. of mol.: 4 / Mutation: C42S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA9, G250, MN / Production host: Komagataella pastoris (fungus) / References: UniProt: Q16790, carbonic anhydrase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-J92 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.47 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: CRYSTALLIZATION CONDITIONS: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2018 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→76.32 Å / Num. obs: 109432 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 36.116 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 15964 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FE2 Resolution: 1.95→76.32 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.107 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / 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: 38.237 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→76.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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