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Yorodumi- PDB-4riu: A Carbonic Anhydrase IX Mimic in Complex with a Saccharin-Based I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4riu | ||||||
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Title | A Carbonic Anhydrase IX Mimic in Complex with a Saccharin-Based Inhibitor | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | Lyase/Lyase inhibitor / Carbonic Anhydrase Fold / Reversible Hydration of CO2 / Active Site Point Mutations / Cytosolic / Lyase-Lyase inhibitor complex | ||||||
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 / morphogenesis of an epithelium / regulation of intracellular pH / 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 / MOLECULAR REPLACEMENT / Resolution: 1.651 Å | ||||||
Authors | Mahon, B.P. / McKenna, R. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2015 Title: Saccharin: A lead compound for structure-based drug design of carbonic anhydrase IX inhibitors. Authors: Mahon, B.P. / Hendon, A.M. / Driscoll, J.M. / Rankin, G.M. / Poulsen, S.A. / Supuran, C.T. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4riu.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4riu.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 4riu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/4riu ftp://data.pdbj.org/pub/pdb/validation_reports/ri/4riu | HTTPS FTP |
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-Related structure data
Related structure data | 4rivC 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
#1: Protein | Mass: 29200.887 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 / References: UniProt: P00918, carbonic anhydrase | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Chemical | ChemComp-3QR / [ | #5: 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: 2.07 Å3/Da / Density % sol: 40.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 1.6 M Sodium Citrate, 50mM Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 4, 2014 |
Radiation | Monochromator: Varimax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→19.87 Å / Num. obs: 27169 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 1.651→19.859 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.651→19.859 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -5.3799 Å / Origin y: -1.3636 Å / Origin z: 85.669 Å
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Refinement TLS group | Selection details: all |