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Yorodumi- PDB-5fl6: Three dimensional structure of human carbonic anhydrase IX in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fl6 | ||||||
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Title | Three dimensional structure of human carbonic anhydrase IX in complex with 5-(1-(4-Methylphenyl)-1H-1,2,3-triazol-4-yl)thiophene-2- sulfonamide | ||||||
Components | CARBONIC ANHYDRASE IX | ||||||
Keywords | LYASE / CARBONIC ANHYDRASE IX / CARBONIC ANHYDRASE 9 / CA IX / CA 9 | ||||||
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. / Zalubovskis, R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: An Efficient Expression and Crystallization System of the Cancer Asociated Carbonic Anhydrase Isoform Ix. Authors: Leitans, J. / Kazaks, A. / Balode, A. / Ivanova, J. / Zalubovskis, R. / Supuran, C.T. / Tars, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fl6.cif.gz | 230.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fl6.ent.gz | 184.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fl6_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5fl6_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5fl6_validation.xml.gz | 50.7 KB | Display | |
Data in CIF | 5fl6_validation.cif.gz | 74.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/5fl6 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/5fl6 | HTTPS FTP |
-Related structure data
Related structure data | 5fl4C 5fl5C 3iaiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 28172.684 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 137-391 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: Q16790, carbonic anhydrase |
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-Non-polymers , 5 types, 1159 molecules
#2: Chemical | ChemComp-Y0R / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: 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: 3.43 Å3/Da / Density % sol: 64.14 % / Description: NONE |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 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) VAPOR ...Details: 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) VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 2, 2015 / Details: MULTILAYER |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.11 Å / Num. obs: 108977 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IAI Resolution: 1.95→48 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.539 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.692 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→48 Å
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Refine LS restraints |
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