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- PDB-6yh5: Crystal structure of chimeric carbonic anhydrase XII with 2-Chlor... -
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Basic information
Entry | Database: PDB / ID: 6yh5 | ||||||
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Title | Crystal structure of chimeric carbonic anhydrase XII with 2-Chloro-4-[(pyrimidin-2-ylsulfanyl)acetyl]benzenesulfonamide | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE / drug design / carbonic anhydrase / benzenesulfonamide / 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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Smirnov, A. / Manakova, E. / Grazulis, S. | ||||||
![]() | ![]() Title: Switching the Inhibitor-Enzyme Recognition Profile via Chimeric Carbonic Anhydrase XII. Authors: Smirnoviene, J. / Smirnov, A. / Zaksauskas, A. / Zubriene, A. / Petrauskas, V. / Mickeviciute, A. / Michailoviene, V. / Capkauskaite, E. / Manakova, E. / Grazulis, S. / Baranauskiene, L. / ...Authors: Smirnoviene, J. / Smirnov, A. / Zaksauskas, A. / Zubriene, A. / Petrauskas, V. / Mickeviciute, A. / Michailoviene, V. / Capkauskaite, E. / Manakova, E. / Grazulis, S. / Baranauskiene, L. / Chen, W.Y. / Ladbury, J.E. / 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 | ![]() | 137.6 KB | Display | ![]() |
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PDB format | ![]() | 104.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yh4C ![]() 6yh6C ![]() 6yh7C ![]() 6yh8C ![]() 6yh9C ![]() 6yhaC ![]() 6yhbC ![]() 6yhcC ![]() 4q09S 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29220.879 Da / Num. of mol.: 1 / Mutation: A65S, N67K, I91T, F130A, V134S, L203N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 338 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/E1F.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/E1F.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-E1F / |
#4: Chemical | ChemComp-BEZ / |
#5: Chemical | ChemComp-DMS / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Crystallization buffer was 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 / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.826605 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→69.672 Å / Num. all: 73229 / Num. obs: 73229 / % possible obs: 98.8 % / Redundancy: 6.8 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Rsym value: 0.049 / Net I/av σ(I): 8.2 / Net I/σ(I): 15.3 / Num. measured all: 494667 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Q09 Resolution: 1.2→40.65 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU R Cruickshank DPI: 0.0369 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.039 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.48 Å2 / Biso mean: 17.055 Å2 / Biso min: 6.93 Å2
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Refinement step | Cycle: final / Resolution: 1.2→40.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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