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Yorodumi- PDB-5clu: THE CRYSTAL STRUCTURE OF THE COMPLEX of HCAII WITH A SACCHARINE D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5clu | ||||||
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Title | THE CRYSTAL STRUCTURE OF THE COMPLEX of HCAII WITH A SACCHARINE DERIVATIVE | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / CARBONIC ANHYDRASE II | ||||||
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: 1.55 Å | ||||||
Authors | D'Ambrosio, K. / De Simone, G. | ||||||
Citation | Journal: Chemistry / Year: 2016 Title: A Combined Crystallographic and Theoretical Study Explains the Capability of Carboxylic Acids to Adopt Multiple Binding Modes in the Active Site of Carbonic Anhydrases. Authors: Langella, E. / D'Ambrosio, K. / D'Ascenzio, M. / Carradori, S. / Monti, S.M. / Supuran, C.T. / 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 | 5clu.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5clu.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 5clu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/5clu ftp://data.pdbj.org/pub/pdb/validation_reports/cl/5clu | HTTPS FTP |
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-Related structure data
Related structure data | 1ca2S 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: 28932.641 Da / Num. of mol.: 1 / Fragment: UNP residues 4-260 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-S8A / ( |
#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: 2.1 Å3/Da / Density % sol: 41.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.5 M (NH4)2SO4, 0.3 M NaCl, 100 mM Tris-HCl (pH 8.2) Temp details: 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 23, 2014 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 32510 / % possible obs: 92.3 % / Redundancy: 4.7 % / Rsym value: 0.063 / Net I/σ(I): 18.16 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.55 / % possible all: 75.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1CA2 Resolution: 1.55→50 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.55→50 Å
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