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Yorodumi- PDB-4pzh: Crystal structure of human carbonic anhydrase isozyme II with 2,3... -
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-Basic information
Entry | Database: PDB / ID: 4pzh | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme II with 2,3,5,6-tetrafluoro-4[(2-hydroxyethyl)sulfonyl]benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / 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 / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / 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 / molecular replacement / Resolution: 1.06 Å | ||||||
Authors | Smirnov, A. / Manakova, E. / Grazulis, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Discovery and characterization of novel selective inhibitors of carbonic anhydrase IX. Authors: Dudutiene, V. / Matuliene, J. / Smirnov, A. / Timm, D.D. / Zubriene, A. / Baranauskiene, L. / Morkunaite, V. / Smirnoviene, J. / Michailoviene, V. / Juozapaitiene, V. / Mickeviciute, A. / ...Authors: Dudutiene, V. / Matuliene, J. / Smirnov, A. / Timm, D.D. / Zubriene, A. / Baranauskiene, L. / Morkunaite, V. / Smirnoviene, J. / Michailoviene, V. / Juozapaitiene, V. / Mickeviciute, A. / Kazokaite, J. / Baksyte, S. / Kasiliauskaite, A. / Jachno, J. / Revuckiene, J. / Kisonaite, M. / Pilipuityte, V. / Ivanauskaite, E. / Milinaviciute, G. / Smirnovas, V. / Petrikaite, V. / Kairys, V. / Petrauskas, V. / Norvaisas, P. / Linge, D. / Gibieza, P. / Capkauskaite, E. / Zaksauskas, A. / Kazlauskas, E. / Manakova, E. / Grazulis, S. / Ladbury, J.E. / Matulis, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pzh.cif.gz | 137.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pzh.ent.gz | 104.8 KB | Display | PDB format |
PDBx/mmJSON format | 4pzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pzh_validation.pdf.gz | 804.3 KB | Display | wwPDB validaton report |
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Full document | 4pzh_full_validation.pdf.gz | 809.4 KB | Display | |
Data in XML | 4pzh_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 4pzh_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/4pzh ftp://data.pdbj.org/pub/pdb/validation_reports/pz/4pzh | HTTPS FTP |
-Related structure data
Related structure data | 4pyxC 4pyyC 4q06C 4q07C 4q08C 4q09C 4q0lC 3hljS C: citing same article (ref.) 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: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 7 types, 283 molecules
#2: Chemical | ChemComp-EDO / |
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#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-DMS / |
#5: Chemical | ChemComp-BCN / |
#6: Chemical | ChemComp-V13 / |
#7: Chemical | ChemComp-MES / |
#8: 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 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.826606 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: High Heat Load (HHL) Monochromator: Si 111; Large Offset Monochromator (LOM) : Si 311, Si 511 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.826606 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.059→69.517 Å / Num. obs: 100624 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 9.034 Å2 / Rsym value: 0.051 / Net I/σ(I): 15.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB ENTRY 3HLJ Resolution: 1.06→40.82 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.171 / WRfactor Rwork: 0.139 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.927 / SU R Cruickshank DPI: 0.029 / SU Rfree: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.42 Å2 / Biso mean: 16.575 Å2 / Biso min: 6.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.06→40.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.059→1.087 Å / Total num. of bins used: 20
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