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- PDB-5amg: Three dimensional structure of human carbonic anhydrase II in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5amg | ||||||
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Title | Three dimensional structure of human carbonic anhydrase II in complex with 2-(Pentylsulfamoyl)-4-sulfamoylbenzoic acid | ||||||
![]() | CARBONIC ANHYDRASE 2 | ||||||
![]() | LYASE / CA II / CA 2 | ||||||
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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leitans, J. / Tars, K. / Zalubovskis, R. | ||||||
![]() | ![]() Title: X-Ray Crystallography-Promoted Drug Design of Carbonic Anhydrase Inhibitors. Authors: Ivanova, J. / Leitans, J. / Tanc, M. / Kazaks, A. / Zalubovskis, R. / Supuran, C.T. / Tars, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.9 KB | Display | ![]() |
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PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 722.3 KB | Display | ![]() |
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Full document | ![]() | 723.5 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5amdC ![]() 5amlC ![]() 4bf1S C: citing same article ( S: Starting model for refinement |
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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: 29157.863 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-IW7 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 1,54 M SODIUM CITRATE 60 MM TRIS- HCL, PH 9.0, PROTEIN 10 MG/ML 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) VAPOR DIFFUSION, SITTING DROP, ...Details: 1,54 M SODIUM CITRATE 60 MM TRIS- HCL, PH 9.0, PROTEIN 10 MG/ML 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, TIME 2-5 DAYS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 26, 2013 / Details: MULTILAYER |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. obs: 34263 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BF1 Resolution: 1.55→69.68 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.958 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.093 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.532 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→69.68 Å
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Refine LS restraints |
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