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Yorodumi- PDB-5n0d: Crystal structure of human carbonic anhydrase II in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n0d | ||||||
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Title | Crystal structure of human carbonic anhydrase II in complex with (R)-4-(6,7-dihydroxy-1-phenyl-3,4-tetrahydroisoquinoline-1H-2-carbonyl)benzenesulfonamide. | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / carbonic anhydrase / benzesulfonamide / protein-inhibitor adduct | ||||||
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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Di Fiore, A. / De Simone, G. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Probing Molecular Interactions between Human Carbonic Anhydrases (hCAs) and a Novel Class of Benzenesulfonamides. Authors: Bruno, E. / Buemi, M.R. / Di Fiore, A. / De Luca, L. / Ferro, S. / Angeli, A. / Cirilli, R. / Sadutto, D. / Alterio, V. / Monti, S.M. / Supuran, C.T. / De Simone, G. / Gitto, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n0d.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n0d.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 5n0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n0d_validation.pdf.gz | 775.7 KB | Display | wwPDB validaton report |
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Full document | 5n0d_full_validation.pdf.gz | 777.7 KB | Display | |
Data in XML | 5n0d_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 5n0d_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/5n0d ftp://data.pdbj.org/pub/pdb/validation_reports/n0/5n0d | HTTPS FTP |
-Related structure data
Related structure data | 5n0eC 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
#1: Protein | Mass: 29477.307 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-8F2 / ( |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-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: 40.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.3 M sodium citrate, 0.1 M Tris-HCl, pH 8.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25.3 Å / Num. obs: 26226 / % possible obs: 97.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.7 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1CA2 Resolution: 1.7→25.3 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 12.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→25.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.72 Å / Total num. of bins used: 24 /
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