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Yorodumi- PDB-3myq: Crystal structure of human carbonic anhydrase isozyme II with 2-c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3myq | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme II with 2-chloro-5-[(1H-imidazo[4,5-c]quinolin-2-ylsulfanyl)acetyl]benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / drug design / carbonic anhydrase / benzenesulfonamide | ||||||
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: 1.35 Å | ||||||
Authors | Grazulis, S. / Manakova, E. / Golovenko, D. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2010 Title: Indapamide-like benzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, and XIII. Authors: Baranauskiene, L. / Golovenko, D. / Manakova, E. / Grazulis, S. / Tumkevicius, S. / Matulis, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3myq.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3myq.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 3myq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3myq_validation.pdf.gz | 798.8 KB | Display | wwPDB validaton report |
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Full document | 3myq_full_validation.pdf.gz | 805.2 KB | Display | |
Data in XML | 3myq_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 3myq_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/3myq ftp://data.pdbj.org/pub/pdb/validation_reports/my/3myq | HTTPS FTP |
-Related structure data
Related structure data | 3m67C 3m96C 3hljS 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
-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 , 5 types, 258 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-MES / | ||||
#4: Chemical | #5: Chemical | ChemComp-E27 / | #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: 2.03 Å3/Da / Density % sol: 39.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Crystallization buffer was 0.1M sodium BICINE, pH 9.0, 0.2 M ammonium sulfate, and 2M sodium malonate, pH 7.0 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: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9443 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 17, 2009 |
Radiation | Monochromator: Double crystal Si(111), horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9443 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→28.843 Å / Num. all: 51791 / Num. obs: 50807 / % possible obs: 98.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 13.44955 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.6 / Num. measured all: 18500 / Num. unique all: 7244 / Rsym value: 0.229 / % possible all: 97 |
-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: 1.35→25.12 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.141 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.907 / SU B: 1.643 / SU ML: 0.031 / SU R Cruickshank DPI: 0.061 / SU Rfree: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: 45.47 Å2 / Biso mean: 16.232 Å2 / Biso min: 3.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→25.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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