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Yorodumi- PDB-4yxo: Human Carbonic Anhydrase II complexed with an inhibitor with a be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yxo | ||||||
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Title | Human Carbonic Anhydrase II complexed with an inhibitor with a benzenesulfonamide group (3). | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å | ||||||
Authors | Rechlin, C. / Heine, A. / Klebe, G. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2016 Title: Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies. Authors: Gaspari, R. / Rechlin, C. / Heine, A. / Bottegoni, G. / Rocchia, W. / Schwarz, D. / Bomke, J. / Gerber, H.D. / Klebe, G. / Cavalli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yxo.cif.gz | 130.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yxo.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 4yxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/4yxo ftp://data.pdbj.org/pub/pdb/validation_reports/yx/4yxo | HTTPS FTP |
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-Related structure data
Related structure data | 4yx4C 4yxiC 4yxuC 4yytC 1cniS 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
-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.) Homo sapiens (human) / Gene: CA2 / Plasmid: PGEX-4T1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 240 molecules
#2: Chemical | ChemComp-MBO / | ||
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#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 2.5 uL of the protein solution (10 mg/ml hCAII in 50 mM Tris pH 7.8) were mixed with 2.5 uL of the well solution (2.7 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with p- ...Details: 2.5 uL of the protein solution (10 mg/ml hCAII in 50 mM Tris pH 7.8) were mixed with 2.5 uL of the well solution (2.7 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with p-chloromercurybenzoicacid) and placed as a hanging drop. Crystals appeared after several days. The crystals were soaked in 3.0 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with the inhibitor, for 1 day. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→50 Å / Num. obs: 108590 / % possible obs: 98 % / Redundancy: 3.63 % / Biso Wilson estimate: 8.578 Å2 / Rsym value: 0.077 / Net I/σ(I): 9.07 |
Reflection shell | Resolution: 1.06→1.12 Å / Redundancy: 3.55 % / Mean I/σ(I) obs: 2.07 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CNI Resolution: 1.06→35.05 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 15.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.06→35.05 Å
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Refine LS restraints |
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LS refinement shell |
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