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Yorodumi- PDB-5drs: Crystal structure of human carbonic anhydraseisozyme II with 3-[(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5drs | ||||||
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Title | Crystal structure of human carbonic anhydraseisozyme II with 3-[(1S)-2,3-Dihydro-1H-inden-1-ylamino]-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / 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 / 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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å | ||||||
Authors | Smirnov, A. / Manakova, E. / Grazulis, S. | ||||||
Citation | Journal: ChemMedChem / Year: 2017 Title: Intrinsic Thermodynamics and Structures of 2,4- and 3,4-Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases. Authors: Zubriene, A. / Smirnov, A. / Dudutiene, V. / Timm, D.D. / Matuliene, J. / Michailoviene, V. / Zaksauskas, A. / Manakova, E. / Grazulis, 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 | 5drs.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5drs.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 5drs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/5drs ftp://data.pdbj.org/pub/pdb/validation_reports/dr/5drs | HTTPS FTP |
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-Related structure data
Related structure data | 5dogC 5dohC 5e2mC 5e2nC 5eheC 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 / Fragment: human carbonic anhydrase II Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 6 types, 255 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-BCN / |
#4: Chemical | ChemComp-DMS / |
#5: Chemical | ChemComp-MES / |
#6: Chemical | ChemComp-5EF / |
#7: 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: 1.99 Å3/Da / Density % sol: 37.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Crystallization buffer: 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 |
-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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.826606 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.099→40.891 Å / Num. all: 91906 / Num. obs: 91906 / % possible obs: 95.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 9.518 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Rsym value: 0.045 / Net I/av σ(I): 4.139 / Net I/σ(I): 19.1 / Num. measured all: 573687 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 3HLJ Resolution: 1.1→40.74 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.18 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.923 / SU R Cruickshank DPI: 0.034 / SU Rfree: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.034 / 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: 136.59 Å2 / Biso mean: 17.214 Å2 / Biso min: 6.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→40.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.099→1.128 Å / Total num. of bins used: 20
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