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- PDB-6otk: Carbonic Anhydrase IX mimic complexed with ureido benzene sulfona... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6otk | ||||||
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Title | Carbonic Anhydrase IX mimic complexed with ureido benzene sulfonamide MB10-596B | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE/LYASE INHIBITOR / ureido benzene sulfonamide / carbonic anhydrase / inhibitor / LYASE / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kota, A. / McKenna, R. | ||||||
![]() | ![]() Title: Carbonic Anhydrase IX mimic complexed with ureido benzene sulfonamide MB9-561B Authors: Kota, A. / McKenna, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.5 KB | Display | ![]() |
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PDB format | ![]() | 95.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 699.4 KB | Display | ![]() |
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Full document | ![]() | 701.8 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6otiC ![]() 6otmC ![]() 6otpC ![]() 6oufC ![]() 3ks3S 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: 28844.465 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-N7S / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M Sodium Citrate, 50mM Tris-HCl, pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.86 Å / Relative weight: 1 |
Reflection | Resolution: 1.123→39.77 Å / Num. obs: 85803 / % possible obs: 92.65 % / Redundancy: 3.3 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.124→1.164 Å / Rmerge(I) obs: 0.75 / Num. unique obs: 6881 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KS3 Resolution: 1.123→39.768 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.36 Å2 / Biso mean: 18.5047 Å2 / Biso min: 6.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.123→39.768 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: -30.1728 Å / Origin y: -1.8829 Å / Origin z: 15.9681 Å
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Refinement TLS group |
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