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Yorodumi- PDB-7agn: Human carbonic anhydrase II in complex with 4-(2-aminoethylsulfan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7agn | ||||||
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Title | Human carbonic anhydrase II in complex with 4-(2-aminoethylsulfanyl)-2,3,5,6-tetrafluoro-N-methyl-benzenesulfonamide | ||||||
Components | carbonic anhydrase 2 | ||||||
Keywords | LYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-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 / 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: 1.15 Å | ||||||
Authors | Paketuryte, V. / Smirnov, A. / Manakova, E. / Grazulis, S. | ||||||
Citation | Journal: Eur.Biophys.J. / Year: 2021 Title: Structure and mechanism of secondary sulfonamide binding to carbonic anhydrases. Authors: Baronas, D. / Dudutiene, V. / Paketuryte, V. / Kairys, V. / Smirnov, A. / Juozapaitiene, V. / Vaskevicius, A. / Manakova, E. / Grazulis, S. / Zubriene, A. / Matulis, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7agn.cif.gz | 494.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7agn.ent.gz | 405.8 KB | Display | PDB format |
PDBx/mmJSON format | 7agn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7agn_validation.pdf.gz | 448 KB | Display | wwPDB validaton report |
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Full document | 7agn_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 7agn_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 7agn_validation.cif.gz | 44.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/7agn ftp://data.pdbj.org/pub/pdb/validation_reports/ag/7agn | HTTPS FTP |
-Related structure data
Related structure data | 7aeqC 7aesC 4ht0S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 1352 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-RAK / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-BCN / #6: Water | ChemComp-HOH / | |
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-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: 2.06 Å3/Da / Density % sol: 40.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.147→79.421 Å / Num. all: 296762 / Num. obs: 296762 / % possible obs: 88.6 % / Redundancy: 3.6 % / Rpim(I) all: 0.068 / Rrim(I) all: 0.132 / Rsym value: 0.102 / Net I/av σ(I): 1.9 / Net I/σ(I): 4.3 / Num. measured all: 1062546 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HT0 Resolution: 1.15→69.65 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.85 Å2 / Biso mean: 16.849 Å2 / Biso min: 4.93 Å2
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Refinement step | Cycle: final / Resolution: 1.15→69.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.177 Å / Rfactor Rfree error: 0
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