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- PDB-3oim: Human Carbonic anhydrase II bound by 2-Ethylestradiol 3-O-sulfamate -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oim | ||||||
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Title | Human Carbonic anhydrase II bound by 2-Ethylestradiol 3-O-sulfamate | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE / 2-ethylestrone / estradiol / sulfamate / mixed alpha-beta / Carbon Dioxide/Bicarbonate conversion | ||||||
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 | ![]() ![]() | ||||||
![]() | Sippel, K.H. / Stander, B.A. / Robbins, A.H. / Tu, C.K. / Agbandje-McKenna, M. / Silverman, D.N. / Joubert, A.M. / McKenna, R. | ||||||
![]() | ![]() Title: Characterization of Carbonic Anhydrase Isozyme Specific Inhibition by Sulfamated 2-Ethylestra Compounds Authors: Sippel, K.H. / Stander, B.A. / Robbins, A.H. / Tu, C.K. / Agbandje-McKenna, M. / Silverman, D.N. / Joubert, A.M. / McKenna, R. #1: ![]() Title: Structures of human carbonic anhydrase II/inhibitor complexes reveal a second binding site for steroidal and nonsteroidal inhibitors. Authors: Cozier, G.E. / Leese, M.P. / Lloyd, M.D. / Baker, M.D. / Thiyagarajan, N. / Acharya, K.R. / Potter, B.V. #2: ![]() Title: Design of a carbonic anhydrase IX active-site mimic to screen inhibitors for possible anticancer properties. Authors: Genis, C. / Sippel, K.H. / Case, N. / Cao, W. / Avvaru, B.S. / Tartaglia, L.J. / Govindasamy, L. / Tu, C. / Agbandje-McKenna, M. / Silverman, D.N. / Rosser, C.J. / 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 | ![]() | 133.6 KB | Display | ![]() |
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PDB format | ![]() | 103 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.8 KB | Display | ![]() |
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Full document | ![]() | 764.5 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3oikC ![]() 3oilC ![]() 3okuC ![]() 3okvC ![]() 2iliS 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 , 5 types, 307 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/VZ5.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/VZ5.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-VZ5 / ( |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-DMS / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.4 M Sodium Citrate, 100 mM Tris, 7.5 mM 2-Ethylestradiol 3-O-sulfamate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 5, 2010 / Details: osmic mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→50 Å / Num. all: 39949 / Num. obs: 39564 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.045 / Net I/σ(I): 29.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2ili Resolution: 1.45→23.763 Å / SU ML: 0.2 / Isotropic thermal model: TLS / σ(F): 0 / Phase error: 14.65 / Stereochemistry target values: ML Details: Individual coordinate, individual isotropic ADP, TLS, occupancy, hydrogen writing
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Solvent computation | Shrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.403 Å2 / ksol: 0.483 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.45→23.763 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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