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Yorodumi- PDB-6rri: Human Carbonic Anhydrase II in complex with fluorinated benzenesu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rri | ||||||
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Title | Human Carbonic Anhydrase II in complex with fluorinated benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Inhibitor / complex / CO2 conversion | ||||||
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: 1.097 Å | ||||||
Authors | Gloeckner, S. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Biomolecules / Year: 2020 Title: The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II. Authors: Glockner, S. / Ngo, K. / Wagner, B. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rri.cif.gz | 191 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rri.ent.gz | 154.2 KB | Display | PDB format |
PDBx/mmJSON format | 6rri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/6rri ftp://data.pdbj.org/pub/pdb/validation_reports/rr/6rri | HTTPS FTP |
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-Related structure data
Related structure data | 6rh4C 6ritC 6rjjC 6rknC 6rl9C 6rnpC 6robC 6roeC 6rqiC 6rrgC 6rs5C 6rszC 6s9gC 6sd7C 3ks3S 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29806.588 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The first 5 amino acids (GSPEF) are remnants of an expression tag. Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus / References: UniProt: P00918, carbonic anhydrase |
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-Sugars , 2 types, 2 molecules
#6: Sugar | ChemComp-GLC / |
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#7: Sugar | ChemComp-BGC / |
-Non-polymers , 5 types, 250 molecules
#2: Chemical | ChemComp-ZN / | ||
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#3: Chemical | ChemComp-HG / | ||
#4: Chemical | ChemComp-BE7 / ( | ||
#5: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: Ammonium sulfate 2.7 M, TRIS 0.1 M, saturated with para-Chloromercuribenzoic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 3, 2017 / Details: Sagitally bended Si(111) crystal |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.097→41.425 Å / Num. obs: 97931 / % possible obs: 98.8 % / Redundancy: 3.58 % / Biso Wilson estimate: 9.9 Å2 / CC1/2: 0.999 / Rsym value: 0.05 / Net I/σ(I): 12.32 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 3.55 % / Mean I/σ(I) obs: 2.49 / Num. unique obs: 15202 / CC1/2: 0.821 / Rsym value: 0.435 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 1.097→22.877 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.097→22.877 Å
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Refine LS restraints |
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LS refinement shell |
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