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Yorodumi- PDB-6ufb: Carbonic anhydrase 2 with inhibitor (2Z)-2-benzylidene-3-oxo-N-(4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ufb | ||||||
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Title | Carbonic anhydrase 2 with inhibitor (2Z)-2-benzylidene-3-oxo-N-(4-sulfamoylphenyl)butanamide (11a/D1) | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / carbonic anhydrase / inhibitor / complex / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Peat, T.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of Potent Dual-Tailed Benzenesulfonamide Inhibitors of Human Carbonic Anhydrases Implicated in Glaucoma and in Vivo Profiling of Their Intraocular Pressure-Lowering Action. Authors: Fares, M. / Eldehna, W.M. / Bua, S. / Lanzi, C. / Lucarini, L. / Masini, E. / Peat, T.S. / Abdel-Aziz, H.A. / Nocentini, A. / Keller, P.A. / Supuran, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ufb.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ufb.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ufb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ufb_validation.pdf.gz | 349.4 KB | Display | wwPDB validaton report |
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Full document | 6ufb_full_validation.pdf.gz | 350.5 KB | Display | |
Data in XML | 6ufb_validation.xml.gz | 1.7 KB | Display | |
Data in CIF | 6ufb_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/6ufb ftp://data.pdbj.org/pub/pdb/validation_reports/uf/6ufb | HTTPS FTP |
-Related structure data
Related structure data | 6ufcC 6ufdC 4cq0S 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
-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 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 6 types, 264 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-Q64 / ( | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-CL / | #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: 41.19 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 200 nL 7 mg/mL protein + 200 nL reservoir solution (2.5-2.8 M ammonium sulfate, 100 mM Tris, pH 8.5-9.0) PH range: 8.5-8.9 |
-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: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 22, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→41.48 Å / Num. obs: 27672 / % possible obs: 97.3 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.036 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.67→1.7 Å / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 9662 / CC1/2: 0.8 / Rpim(I) all: 0.302 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4CQ0 Resolution: 1.67→41.035 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.901 / SU ML: 0.063 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.098 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.896 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→41.035 Å
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Refine LS restraints |
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LS refinement shell |
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