+Open data
-Basic information
Entry | Database: PDB / ID: 7m23 | ||||||
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Title | Human carbonic anhydrase II in complex with troglitazone | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / glitazone drug class / 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 / 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: 1.3 Å | ||||||
Authors | Mueller, S.L. / Peat, T.S. | ||||||
Citation | Journal: Molecules / Year: 2021 Title: The Glitazone Class of Drugs as Carbonic Anhydrase Inhibitors-A Spin-Off Discovery from Fragment Screening. Authors: Mueller, S.L. / Chrysanthopoulos, P.K. / Halili, M.A. / Hepburn, C. / Nebl, T. / Supuran, C.T. / Nocentini, A. / Peat, T.S. / Poulsen, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m23.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m23.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 7m23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m23_validation.pdf.gz | 686.1 KB | Display | wwPDB validaton report |
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Full document | 7m23_full_validation.pdf.gz | 687.2 KB | Display | |
Data in XML | 7m23_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 7m23_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/7m23 ftp://data.pdbj.org/pub/pdb/validation_reports/m2/7m23 | HTTPS FTP |
-Related structure data
Related structure data | 7m24C 7m26C 6odzS S: Starting model for refinement C: citing same article (ref.) |
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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: 29070.785 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-TDZ / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: Protein concentration was 4 mg/mL; equal volumes (250 nL) of protein plus reservoir were added to the plate; the reservoir was 1.5 M tri-potassium citrate, 0.1 M tris buffer at pH 8.3. 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: MX1 / Wavelength: 0.953656 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953656 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→41.29 Å / Num. obs: 58740 / % possible obs: 99.1 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.3→1.32 Å / Rmerge(I) obs: 0.627 / Num. unique obs: 2886 / CC1/2: 0.825 / Rpim(I) all: 0.416 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6odz Resolution: 1.3→39.943 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.552 / SU ML: 0.029 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.043 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: 14.036 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→39.943 Å
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Refine LS restraints |
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LS refinement shell |
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