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Yorodumi- PDB-5fdc: Crystal structure of Human Carbonic Anhydrase II in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fdc | ||||||
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Title | Crystal structure of Human Carbonic Anhydrase II in complex with the anticonvulsant sulfamide JNJ-26990990 and its S,S-dioxide analog. | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Sulfamide Inhibitor / Protein-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 / FOURIER SYNTHESIS / Resolution: 1.75 Å | ||||||
Authors | Di Fiore, A. / De Simone, G. / Alterio, V. / Riccio, V. / Winum, J.-Y. / Carta, F. / Supuran, C.T. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2016 Title: The anticonvulsant sulfamide JNJ-26990990 and its S,S-dioxide analog strongly inhibit carbonic anhydrases: solution and X-ray crystallographic studies. Authors: Di Fiore, A. / De Simone, G. / Alterio, V. / Riccio, V. / Winum, J.Y. / Carta, F. / 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 | 5fdc.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fdc.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fdc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/5fdc ftp://data.pdbj.org/pub/pdb/validation_reports/fd/5fdc | HTTPS FTP |
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-Related structure data
Related structure data | 5fdiC 1ca2S 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 268 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-5WN / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-HGB / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.5 M ammonium sulphate, 0.3 M sodium chloride, 0.1 M Tris-HCl, pH 8.4 and 5 mM 4-(hydroxymercurybenzoate) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 23860 / % possible obs: 97.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.26 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.258 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1CA2 Resolution: 1.75→20 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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