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Yorodumi- PDB-4yvy: Crystal structure of human carbonic anhydrase II in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yvy | ||||||
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Title | Crystal structure of human carbonic anhydrase II in complex with hydroxylamine-O-sulfonamide, a molecule incorporating two zinc-binding groups. | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Protein-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 / 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 / FOURIER SYNTHESIS / Resolution: 1.45 Å | ||||||
Authors | Di Fiore, A. / De Simone, G. | ||||||
Citation | Journal: To Be Published Title: A VERSATILE ZINC-BINDING GROUP FOR CARBONIC ANHYDRASE INHIBITORS Authors: Di Fiore, A. / Vergara, A. / Caterino, M. / Alterio, V. / Monti, S.M. / Ombouma, J. / Dumy, P. / Vullo, D. / Supurand, C.T. / Winum, J.-Y. / De Simone, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yvy.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yvy.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 4yvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/4yvy ftp://data.pdbj.org/pub/pdb/validation_reports/yv/4yvy | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 29157.863 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 (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-4J3 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.3 M sodium citrate and 0.1 M Tris-HCl, pH 8.5 / PH range: 8.0-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 39182 / % possible obs: 91.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.64 |
Reflection shell | Highest resolution: 1.45 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.81 / % possible all: 74.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→50 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.45→50 Å
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