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Yorodumi- PDB-5sz1: Carbonic anhydrase II in complex with 4-(2-methylphenyl)-benzenes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5sz1 | ||||||
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Title | Carbonic anhydrase II in complex with 4-(2-methylphenyl)-benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / sulfonamide / inhibitor / zinc-binding / LYASE-LYASE INHIBITOR complex | ||||||
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 / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Bhatt, A. / Mahon, B.P. / Cornelio, B. / McKenna, R. | ||||||
Citation | Journal: Chembiochem / Year: 2017 Title: Structure-Activity Relationships of Benzenesulfonamide-Based Inhibitors towards Carbonic Anhydrase Isoform Specificity. Authors: Bhatt, A. / Mahon, B.P. / Cruzeiro, V.W. / Cornelio, B. / Laronze-Cochard, M. / Ceruso, M. / Sapi, J. / Rance, G.A. / Khlobystov, A.N. / Fontana, A. / Roitberg, A. / Supuran, C.T. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sz1.cif.gz | 130.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sz1.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 5sz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5sz1_validation.pdf.gz | 457.1 KB | Display | wwPDB validaton report |
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Full document | 5sz1_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 5sz1_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 5sz1_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/5sz1 ftp://data.pdbj.org/pub/pdb/validation_reports/sz/5sz1 | HTTPS FTP |
-Related structure data
Related structure data | 5sz0C 5sz2C 5sz3C 5sz4C 5sz5C 5sz6C 5sz7C 3ks3S 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: 28932.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 244 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-72E / | #6: 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: 2.1 Å3/Da / Density % sol: 41.39 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 1.6M Sodium Citrate, 50mM Tris pH 7.8 / PH range: 7.2-8.2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 15, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→20 Å / Num. obs: 33928 / % possible obs: 96.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 15.55 Å2 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.025 / Rrim(I) all: 0.051 / Χ2: 0.875 / Net I/av σ(I): 27.323 / Net I/σ(I): 13.4 / Num. measured all: 131481 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ks3 Resolution: 1.55→19.915 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.15 Å2 / Biso mean: 18.9588 Å2 / Biso min: 7.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→19.915 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: -5.9834 Å / Origin y: -0.6202 Å / Origin z: 85.6494 Å
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Refinement TLS group |
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