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- PDB-6rhj: Crystal structure of human carbonic anhydrase isozyme II with 4-(... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rhj | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme II with 4-(4-benzyl-1,4-diazepane-1-carbonyl)benzenesulfonamide | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferraroni, M. / Angeli, A. / Supuran, C.T. | ||||||
![]() | ![]() Title: Sulfonamides incorporating piperazine bioisosteres as potent human carbonic anhydrase I, II, IV and IX inhibitors. Authors: Chiaramonte, N. / Bua, S. / Angeli, A. / Ferraroni, M. / Picchioni, I. / Bartolucci, G. / Braconi, L. / Dei, S. / Teodori, E. / Supuran, C.T. / Romanelli, M.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 71.7 KB | Display | ![]() |
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PDB format | ![]() | 50.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6rg3C ![]() 6rg4C ![]() 6rhkC ![]() 4fikS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-K4H / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.85 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.6 sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→69.49 Å / Num. obs: 43292 / % possible obs: 99.4 % / Redundancy: 2.7 % / CC1/2: 0.989 / Rrim(I) all: 0.095 / Rsym value: 0.076 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.44→1.47 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2186 / CC1/2: 0.829 / Rrim(I) all: 0.282 / Rsym value: 0.185 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FIK Resolution: 1.44→69.49 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.368 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.069 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.218 Å2
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Refinement step | Cycle: 1 / Resolution: 1.44→69.49 Å
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Refine LS restraints |
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