+Open data
-Basic information
Entry | Database: PDB / ID: 5j8z | ||||||
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Title | Human carbonic anhydrase II in complex with ligand | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Cytoplasm / 2-Thio-6-oxo-1 / 6-dihydropyrimidines / Sulfonamides | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Alterio, V. / De Simone, G. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2016 Title: Kinetic and X-ray crystallographic investigations of substituted 2-thio-6-oxo-1,6-dihydropyrimidine-benzenesulfonamides acting as carbonic anhydrase inhibitors. Authors: Vullo, D. / Supuran, C.T. / Scozzafava, A. / De Simone, G. / Monti, S.M. / Alterio, V. / Carta, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j8z.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j8z.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 5j8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/5j8z ftp://data.pdbj.org/pub/pdb/validation_reports/j8/5j8z | 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
-Protein , 1 types, 1 molecules A
#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 (bacteria) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 238 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-FC4 / ( |
#5: Chemical | ChemComp-6KE / ( |
#6: 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: 40.64 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.3 M sodium citrate, 0.1 M TRIS-HCl / 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: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 26271 / % possible obs: 97.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.7 / % possible all: 75.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CA2 Resolution: 1.7→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Solvent computation | Bsol: 47.2862 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.58 Å2 / Biso mean: 12.637 Å2 / Biso min: 2.34 Å2
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Refinement step | Cycle: final / Resolution: 1.7→50 Å
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Refine LS restraints |
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