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Yorodumi- PDB-3nb5: Human carbonic anhydrase II in complex with 2-(3-chloro-4-hydroxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nb5 | ||||||
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Title | Human carbonic anhydrase II in complex with 2-(3-chloro-4-hydroxyphenyl)-N-(4-sulfamoylphenethyl)acetamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / drug design / natural product / sulfamate / LYASE-LYASE 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Hofmann, A. / Osman, A. / Davis, R.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Natural Product-Based Phenols as Novel Probes for Mycobacterial and Fungal Carbonic Anhydrases Authors: Davis, R.A. / Hofmann, A. / Osman, A. / Hall, R.A. / Muhlschlegel, F.A. / Vullo, D. / Innocenti, A. / Supuran, C.T. / Poulsen, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nb5.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nb5.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 3nb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/3nb5 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/3nb5 | HTTPS FTP |
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-Related structure data
Related structure data | 3p4vC 3hknS 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: carbonic anhydrase ii / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-R21 / | ||
#4: Chemical | #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: 2.12 Å3/Da / Density % sol: 41.96 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.6M (NH4)2SO4, 0.1M TRIS/HCl, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9544 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9544 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→24.8 Å / Num. obs: 22881 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 11.733 Å2 / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.234 / Num. unique all: 3287 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3HKN Resolution: 1.8→24.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1011777.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.5892 Å2 / ksol: 0.393392 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→24.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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