+Open data
-Basic information
Entry | Database: PDB / ID: 7mu3 | ||||||
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Title | human carbonic anhydrase 9 mimic with compound | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / human carbonic anhydrase II / drug discovery / privileged scaffolds | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Peat, T.S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2021 Title: Privileged scaffolds in medicinal chemistry: Studies on pyrazolo[1,5-a]pyrimidines on sulfonamide containing Carbonic Anhydrase inhibitors. Authors: Gumus, A. / Bozdag, M. / Angeli, A. / Peat, T.S. / Carta, F. / Supuran, C.T. / Selleri, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mu3.cif.gz | 133.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mu3.ent.gz | 99.1 KB | Display | PDB format |
PDBx/mmJSON format | 7mu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mu3_validation.pdf.gz | 733.1 KB | Display | wwPDB validaton report |
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Full document | 7mu3_full_validation.pdf.gz | 735.3 KB | Display | |
Data in XML | 7mu3_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 7mu3_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/7mu3 ftp://data.pdbj.org/pub/pdb/validation_reports/mu/7mu3 | HTTPS FTP |
-Related structure data
Related structure data | 5g03S 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: 29226.859 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 , 6 types, 278 molecules
#2: Chemical | ChemComp-ZN / | ||
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#3: Chemical | ChemComp-ZOA / | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | ChemComp-IMD / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-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: 41.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein at 5.9 mg/mL; 200 nL plus 200 nL drops with the reservoir being 2.7 M ammonium sulfate and 50 mM Tris buffer at pH 8.2 PH range: 8-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953733026981 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953733026981 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→41.61 Å / Num. obs: 52509 / % possible obs: 98.5 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.35→1.37 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2048 / CC1/2: 0.9 / Rpim(I) all: 0.205 / % possible all: 78.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5g03 Resolution: 1.35→40.829 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.491 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.046 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→40.829 Å
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Refine LS restraints |
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LS refinement shell |
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