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Yorodumi- PDB-3n0n: Crystal structure of human carbonic anhydrase II in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 3n0n | ||||||
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Title | Crystal structure of human carbonic anhydrase II in complex with a benzenesulfonamide inhibitor | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / zinc metalloenzyme lyase / benzenesulfonamide inhibitor / zinc ligands / LYASE / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Avvaru, B.S. / Wagner, J. / Robbins, A.H. / McKenna, R. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2010 Title: Selective hydrophobic pocket binding observed within the carbonic anhydrase II active site accommodate different 4-substituted-ureido-benzenesulfonamides and correlate to inhibitor potency. Authors: Pacchiano, F. / Aggarwal, M. / Avvaru, B.S. / Robbins, A.H. / Scozzafava, A. / McKenna, R. / 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 | 3n0n.cif.gz | 171.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n0n.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 3n0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/3n0n ftp://data.pdbj.org/pub/pdb/validation_reports/n0/3n0n | HTTPS FTP |
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-Related structure data
Related structure data | 3mzcSC 3n2pC 3n3jC 3n4bC C: citing same article (ref.) S: Starting model for refinement |
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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: 29289.062 Da / Num. of mol.: 1 / Fragment: human carbonic anhydrase II Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HCA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-P9B / |
#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: 2.09 Å3/Da / Density % sol: 41.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 50 mM tris-HCl, 1.2 M sodium citrate, 5 + 5 uL droplet, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 30, 2009 / Details: mirrors |
Radiation | Monochromator: Rigaku varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 36024 / Num. obs: 36024 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 5.1 / % possible all: 87.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3MZC Resolution: 1.5→19.968 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.16 / σ(F): 0 / Phase error: 14.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.513 Å2 / ksol: 0.467 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→19.968 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.8492 Å / Origin y: -1.7346 Å / Origin z: 16.0414 Å
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Refinement TLS group | Selection details: CHAIN A AND NOT ELEMENT H |