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Yorodumi- PDB-3sax: Crystal structure of human carbonic anhydrase isozyme II with 2-c... -
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-Basic information
Entry | Database: PDB / ID: 3sax | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme II with 2-chloro-5-{[(5-ethyl-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | lyase/lyase inhibitor / drug design / sulfonamide / 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 / 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 / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.1 Å | ||||||
Authors | Grazulis, S. / Manakova, E. / Tamulaitiene, G. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2012 Title: Design of [(2-pyrimidinylthio)acetyl]benzenesulfonamides as inhibitors of human carbonic anhydrases. Authors: Capkauskaite, E. / Zubriene, A. / Baranauskiene, L. / Tamulaitiene, G. / Manakova, E. / Kairys, V. / 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 | 3sax.cif.gz | 164.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sax.ent.gz | 129.1 KB | Display | PDB format |
PDBx/mmJSON format | 3sax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/3sax ftp://data.pdbj.org/pub/pdb/validation_reports/sa/3sax | HTTPS FTP |
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-Related structure data
Related structure data | 3m2nC 3s8xC 3s9tC 3sapC 3sbhC 3sbiC 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 , 5 types, 361 molecules
#2: Chemical | ChemComp-ZN / | ||
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#3: Chemical | ChemComp-E50 / | ||
#4: Chemical | ChemComp-BCN / | ||
#5: Chemical | #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: 2.08 Å3/Da / Density % sol: 40.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1M Na-bicine pH 9, 2.6M Na-malonate pH 7.55, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 12, 2010 / Details: Mirror Bent, vertically focussing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→41.172 Å / Num. obs: 92709 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 7.8 Å2 / Rsym value: 0.068 / Net I/σ(I): 15.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.1→35.49 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.163 / WRfactor Rwork: 0.128 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.93 / SU R Cruickshank DPI: 0.035 / SU Rfree: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 51.87 Å2 / Biso mean: 12.365 Å2 / Biso min: 3.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→35.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.128 Å / Total num. of bins used: 20
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