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Yorodumi- PDB-6gm9: Human Carbonic Anhydrase II in complex with 4-Methylbenzenesulfonamide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gm9 | ||||||
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Title | Human Carbonic Anhydrase II in complex with 4-Methylbenzenesulfonamide | ||||||
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: 1.089 Å | ||||||
Authors | Gloeckner, S. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Conformational Changes in Alkyl Chains Determine the Thermodynamic and Kinetic Binding Profiles of Carbonic Anhydrase Inhibitors. Authors: Glockner, S. / Ngo, K. / Sager, C.P. / Hufner-Wulsdorf, T. / 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 | 6gm9.cif.gz | 185.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gm9.ent.gz | 149.1 KB | Display | PDB format |
PDBx/mmJSON format | 6gm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/6gm9 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/6gm9 | HTTPS FTP |
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-Related structure data
Related structure data | 6gdcC 6hqxC 6hr3C 6hxdC 6i0wC 6i1uC 6i2fC 6i3eC 6sbhC 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 five amino acids (GSPEF) of the sample sequence 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, 3 molecules
#4: Sugar | #7: Sugar | ChemComp-GLC / | |
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-Non-polymers , 5 types, 293 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-HG / | ||||
#5: Chemical | #6: Chemical | ChemComp-MBO / | #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: 40.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: Ammoniumsulfate 2.70 M, pH = 7.8, saturated with p-Chloromercurybenzoic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Si(111) 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: 1.089→41.472 Å / Num. obs: 99517 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.62 % / CC1/2: 0.998 / Rsym value: 0.045 / Net I/σ(I): 15.44 |
Reflection shell | Resolution: 1.089→1.095 Å / Redundancy: 3.64 % / Mean I/σ(I) obs: 5.15 / Num. unique obs: 15508 / CC1/2: 0.956 / Rsym value: 0.2377 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 1.089→23.792 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 8.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.089→23.792 Å
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Refine LS restraints |
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LS refinement shell |
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