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Yorodumi- PDB-3caj: Crystal structure of the human carbonic anhydrase II in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3caj | ||||||
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Title | Crystal structure of the human carbonic anhydrase II in complex with ethoxzolamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Protein-inhibitor complex / Disease mutation / Metal-binding | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Di Fiore, A. / De Simone, G. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: Carbonic anhydrase inhibitors: the X-ray crystal structure of ethoxzolamide complexed to human isoform II reveals the importance of thr200 and gln92 for obtaining tight-binding inhibitors Authors: Di Fiore, A. / Pedone, C. / Antel, J. / Waldeck, H. / Witte, A. / Wurl, M. / Scozzafava, A. / Supuran, C.T. / De Simone, G. #1: Journal: Protein Sci. / Year: 1994 Title: Positions of His-64 and a bound water in human carbonic anhydrase II upon binding three structurally related inhibitors Authors: Smith, G.M. / Alexander, R.S. / Christianson, D.W. / McKeever, B.M. / Ponticello, G.S. / Springer, J.P. / Randall, W.C. / Baldwin, J.J. / Habecker, C.N. #2: Journal: Protein Sci. / Year: 1998 Title: Structures of murine carbonic anhydrase IV and human carbonic anhydrase II complexed with brinzolamide: molecular basis of isozyme-drug discrimination Authors: Stams, T. / Chen, Y. / Boriack-Sjodin, P.A. / Hurt, J.D. / Liao, J. / May, J.A. / Dean, T. / Laipis, P. / Silverman, D.N. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3caj.cif.gz | 73.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3caj.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 3caj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3caj_validation.pdf.gz | 1004.6 KB | Display | wwPDB validaton report |
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Full document | 3caj_full_validation.pdf.gz | 1009.3 KB | Display | |
Data in XML | 3caj_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 3caj_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/3caj ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3caj | HTTPS FTP |
-Related structure data
Related structure data | 1ca2S 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
-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 , 6 types, 308 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-EZL / |
#5: Chemical | ChemComp-MBO / |
#6: Chemical | ChemComp-GOL / |
#7: 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: 2.08 Å3/Da / Density % sol: 40.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 2.5M ammonium sulphate, 0.3M sodium chloride, 0.1M Tris-HCl, 1mM DTT, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 21636 / Num. obs: 21636 / % possible obs: 95.9 % / Redundancy: 3.1 % / Rsym value: 0.061 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 8.4 / Num. unique all: 1780 / Rsym value: 0.134 / % possible all: 80.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1CA2 Resolution: 1.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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