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- PDB-3sap: 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: 3sap | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme II with 4-{[(5-butyl-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | lyase/lyase inhibitor / drug design / sulfonamide / metal-binding / lyase-lyase inhibitor complex | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grazulis, S. / Manakova, E. / Tamulaitiene, G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.8 KB | Display | ![]() |
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PDB format | ![]() | 51.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3m2nC ![]() 3s8xC ![]() 3s9tC ![]() 3saxC ![]() 3sbhC ![]() 3sbiC ![]() 3hljS 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
-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.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 200 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/E2I.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/E2I.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-BCN / |
#4: Chemical | ChemComp-MES / |
#5: Chemical | ChemComp-DMS / |
#6: Chemical | ChemComp-E2I / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.3M Na-bicine pH 9, 2.3M Na-malonate pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Nov 14, 2010 / Details: Detector swing-out angle up to 30 degrees | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8174 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→30.36 Å / Num. obs: 23825 / % possible obs: 99 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 30.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3HLJ Resolution: 1.75→28.89 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 51.24 Å2 / Biso mean: 17.632 Å2 / Biso min: 5.91 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→28.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0.138
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