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Yorodumi- PDB-6got: Crystal structure of human carbonic anhydrase II in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6got | ||||||
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Title | Crystal structure of human carbonic anhydrase II in complex with the inhibitor 4-(phenethylthio)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: 1.56 Å | ||||||
Authors | Ferraroni, M. / Supuran, C.T. / Angeli, A. | ||||||
Citation | Journal: Bioorg. Chem. / Year: 2018 Title: Synthesis of different thio-scaffolds bearing sulfonamide with subnanomolar carbonic anhydrase II and IX inhibitory properties and X-ray investigations for their inhibitory mechanism. Authors: Angeli, A. / Tanini, D. / Capperucci, A. / Malevolti, G. / Turco, F. / Ferraroni, M. / Supuran, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6got.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6got.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 6got.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/6got ftp://data.pdbj.org/pub/pdb/validation_reports/go/6got | HTTPS FTP |
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-Related structure data
Related structure data | 4fikS 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: 29289.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: erytrocytes / Source: (natural) Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Chemical | ChemComp-F6W / | #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: 2.09 Å3/Da / Density % sol: 41.18 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 8 / Details: 1.5 M sodium citrate, Tris 100 mM |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.827 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 13, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.827 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.56→41.11 Å / Num. obs: 33578 / % possible obs: 96.5 % / Redundancy: 4.21 % / CC1/2: 0.99 / Rmerge(I) obs: 0.173 / Rrim(I) all: 0.196 / Net I/σ(I): 5.48 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.56→41.11 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.393 / SU ML: 0.083 / SU R Cruickshank DPI: 0.0992 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.094 / 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: 68.05 Å2 / Biso mean: 15.776 Å2 / Biso min: 7.33 Å2
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Refinement step | Cycle: final / Resolution: 1.56→41.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.601 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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