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Yorodumi- PDB-3okv: Human Carbonic Anhydrase II A65S, N67Q (CA IX mimic) bound with 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3okv | ||||||
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Title | Human Carbonic Anhydrase II A65S, N67Q (CA IX mimic) bound with 2-Ethylestrone 3-O-sulfamate | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Mixes alpha/beta fold / Reversible hydration of Carbon Dioxide to Bicarbonate | ||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Sippel, K.H. / Stander, B.A. / Robbins, A.H. / Tu, C.K. / Agbandje-McKenna, M. / Silverman, D.N. / Joubert, A.M. / McKenna, R. | ||||||
Citation | Journal: LETT.DRUG DES.DISCOVERY / Year: 2011 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: Journal: Biochemistry / Year: 2010 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: Journal: Biochemistry / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3okv.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3okv.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 3okv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3okv_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3okv_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3okv_validation.xml.gz | 17 KB | Display | |
Data in CIF | 3okv_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/3okv ftp://data.pdbj.org/pub/pdb/validation_reports/ok/3okv | HTTPS FTP |
-Related structure data
Related structure data | 3oikC 3oilC 3oimC 3okuC 2iliS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29319.086 Da / Num. of mol.: 1 / Mutation: A65S, N67Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P00918, carbonic anhydrase | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.4 M Sodium citrate, 100mM Tris, 7.5 mM 2-Ethylestrone 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 8, 2010 / Details: Osmic mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 40167 / Num. obs: 40167 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.051 / Net I/σ(I): 28.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ili Resolution: 1.45→28.704 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.15 / Isotropic thermal model: TLS / σ(F): 0 / Phase error: 13.18 / Stereochemistry target values: ML Details: Individual coordinate and ADP refinement, rigid body, TLS, riding hydrogen, occupancy
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Solvent computation | Shrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.33 Å2 / ksol: 0.455 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.45→28.704 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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