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- PDB-4q07: Crystal structure of chimeric carbonic anhydrase IX with inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 4q07 | ||||||
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Title | Crystal structure of chimeric carbonic anhydrase IX with inhibitor | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE/LYASE INHIBITOR / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Smirnov, A. / Manakova, E. / Grazulis, S. | ||||||
![]() | ![]() Title: Discovery and characterization of novel selective inhibitors of carbonic anhydrase IX. Authors: Dudutiene, V. / Matuliene, J. / Smirnov, A. / Timm, D.D. / Zubriene, A. / Baranauskiene, L. / Morkunaite, V. / Smirnoviene, J. / Michailoviene, V. / Juozapaitiene, V. / Mickeviciute, A. / ...Authors: Dudutiene, V. / Matuliene, J. / Smirnov, A. / Timm, D.D. / Zubriene, A. / Baranauskiene, L. / Morkunaite, V. / Smirnoviene, J. / Michailoviene, V. / Juozapaitiene, V. / Mickeviciute, A. / Kazokaite, J. / Baksyte, S. / Kasiliauskaite, A. / Jachno, J. / Revuckiene, J. / Kisonaite, M. / Pilipuityte, V. / Ivanauskaite, E. / Milinaviciute, G. / Smirnovas, V. / Petrikaite, V. / Kairys, V. / Petrauskas, V. / Norvaisas, P. / Linge, D. / Gibieza, P. / Capkauskaite, E. / Zaksauskas, A. / Kazlauskas, E. / Manakova, E. / Grazulis, S. / 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 | ![]() | 161.3 KB | Display | ![]() |
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PDB format | ![]() | 127.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4pyxC ![]() 4pyyC ![]() 4pzhC ![]() 4q06C ![]() 4q08C ![]() 4q09C ![]() 4q0lC ![]() 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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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29242.992 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, I91L, F130V, V134L, L203A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 310 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/V14.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/V14.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-V14 / |
#5: Chemical | ChemComp-BCN / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 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, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: High Heat Load (HHL) Monochromator: Si 111; Large Offset Monochromator (LOM) : Si 311, Si 511 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.826606 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.149→69.862 Å / Num. obs: 77927 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 8.729 Å2 / Rsym value: 0.065 / Net I/σ(I): 8.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.15→69.86 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.173 / WRfactor Rwork: 0.135 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.93 / SU R Cruickshank DPI: 0.043 / SU Rfree: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.041 / 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: 73.25 Å2 / Biso mean: 14.353 Å2 / Biso min: 5.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→69.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.149→1.179 Å / Total num. of bins used: 20
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