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Yorodumi- PDB-5e2r: The crystal structure of the human carbonic anhydrase II in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e2r | ||||||
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Title | The crystal structure of the human carbonic anhydrase II in complex with a 1,1'-biphenyl-4-sulfonamide inhibitor | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / 1'-BIPHENYL-4-SULFONAMIDE / COMPLEX / INHIBITOR | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Alterio, V. / De Simone, G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Discovery of 1,1'-Biphenyl-4-sulfonamides as a New Class of Potent and Selective Carbonic Anhydrase XIV Inhibitors. Authors: La Regina, G. / Coluccia, A. / Famiglini, V. / Pelliccia, S. / Monti, L. / Vullo, D. / Nuti, E. / Alterio, V. / De Simone, G. / Monti, S.M. / Pan, P. / Parkkila, S. / Supuran, C.T. / Rossello, A. / Silvestri, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e2r.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e2r.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 5e2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/5e2r ftp://data.pdbj.org/pub/pdb/validation_reports/e2/5e2r | HTTPS FTP |
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-Related structure data
Related structure data | 5cjfC 1ca2S 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: 29477.307 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-520 / |
#4: Chemical | ChemComp-GOL / |
#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: 40.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: Na-Citrate, Tris-HCl / PH range: 8.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 30330 / % possible obs: 95 % / Redundancy: 4.2 % / Rsym value: 0.052 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 5.8 / % possible all: 75.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1CA2 Resolution: 1.6→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Solvent computation | Bsol: 38.2567 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 42.91 Å2 / Biso mean: 15.6 Å2 / Biso min: 4.58 Å2
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Refinement step | Cycle: final / Resolution: 1.6→50 Å
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Refine LS restraints |
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