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Yorodumi- PDB-6ufd: Carbonic anhydrase 2 with inhibitor (2Z)-3-oxo-N-(4-sulfamoylphen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ufd | ||||||
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Title | Carbonic anhydrase 2 with inhibitor (2Z)-3-oxo-N-(4-sulfamoylphenyl)-2-[(thiophen-2-yl)methylidene]butanamide (11g/D7) | ||||||
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 / 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 / regulation of intracellular pH / morphogenesis of an epithelium / 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: 1.48 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 | 6ufd.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ufd.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ufd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/6ufd ftp://data.pdbj.org/pub/pdb/validation_reports/uf/6ufd | HTTPS FTP |
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-Related structure data
Related structure data | 6ufbC 6ufcC 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 , 5 types, 256 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-Q6D / ( | #5: Chemical | ChemComp-CL / | #6: 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: 2.12 Å3/Da / Density % sol: 41.96 % |
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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) |
-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: 0.9537299871 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537299871 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→41.65 Å / Num. obs: 40433 / % possible obs: 97.7 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.053 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.48→1.5 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1407 / CC1/2: 0.625 / Rpim(I) all: 0.37 / % possible all: 69.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4CQ0 Resolution: 1.48→41.255 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.089 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.065 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: 13.836 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→41.255 Å
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Refine LS restraints |
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LS refinement shell |
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