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Yorodumi- PDB-5sz5: Carbonic anhydrase IX-mimic in complex with 4-(2-methylphenyl)-be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5sz5 | ||||||
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Title | Carbonic anhydrase IX-mimic 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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.274 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 | 5sz5.cif.gz | 170 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sz5.ent.gz | 134.7 KB | Display | PDB format |
PDBx/mmJSON format | 5sz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5sz5_validation.pdf.gz | 442.4 KB | Display | wwPDB validaton report |
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Full document | 5sz5_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 5sz5_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 5sz5_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/5sz5 ftp://data.pdbj.org/pub/pdb/validation_reports/sz/5sz5 | HTTPS FTP |
-Related structure data
Related structure data | 5sz0C 5sz1C 5sz2C 5sz3C 5sz4C 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
#1: Protein | Mass: 28844.465 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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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-72E / |
#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: 2.11 Å3/Da / Density % sol: 41.81 % |
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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: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.274→19.963 Å / Num. obs: 59116 / % possible obs: 98.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 9.43 Å2 / Rmerge(I) obs: 0.112 / Net I/av σ(I): 11.992 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 1.28→1.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.618 / CC1/2: 0.877 / % possible all: 99.5 |
-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: 1.274→19.963 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.99 / 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: 1.274→19.963 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.9436 Å / Origin y: -1.7638 Å / Origin z: 15.8572 Å
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Refinement TLS group | Selection details: all |