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Yorodumi- PDB-5n1s: Crystal structure of human carbonic anhydrase II in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n1s | ||||||
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Title | Crystal structure of human carbonic anhydrase II in complex with the inhibitor 4-(1H-Indol-2-yl)-benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å | ||||||
Authors | Ferraroni, M. / Supuran, C.T. / Scozzafava, A. / Carta, F. | ||||||
Citation | Journal: Inorg.Chim.Acta. / Year: 2018 Title: Sulfonamide carbonic anhydrase inhibitors: Zinc coordination and tail effects influence inhibitory efficacy and selectivity for different isoforms Authors: Ferraroni, M. / Cornelio, B. / Sapi, J. / Supuran, C.T. / Scozzafava, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n1s.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n1s.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 5n1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/5n1s ftp://data.pdbj.org/pub/pdb/validation_reports/n1/5n1s | HTTPS FTP |
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-Related structure data
Related structure data | 5n1rC 5n24C 5n25C 4fikS S: Starting model for refinement C: citing same article (ref.) |
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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: 29289.062 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) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-8GE / |
#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: 2.08 Å3/Da / Density % sol: 40.97 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 8 / Details: 1.5 M sodium citrate, Tris 50 mM |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97974 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97974 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→30 Å / Num. obs: 63363 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 2.845 % / Biso Wilson estimate: 15.167 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.07 / Χ2: 0.973 / Net I/σ(I): 11.86 / Num. measured all: 180261 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4FIK Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.797 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0488 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.051 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.85 Å2 / Biso mean: 13.328 Å2 / Biso min: 4.2 Å2
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Refinement step | Cycle: final / Resolution: 1.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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