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Yorodumi- PDB-3c7p: Crystal structure of human carbonic anhydrase II in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c7p | ||||||
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Title | Crystal structure of human carbonic anhydrase II in complex with STX237 | ||||||
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: 1.7 Å | ||||||
Authors | Di Fiore, A. / De Simone, G. | ||||||
Citation | Journal: Mol.Cancer Ther. / Year: 2008 Title: Anticancer steroid sulfatase inhibitors: synthesis of a potent fluorinated second-generation agent, in vitro and in vivo activities, molecular modeling, and protein crystallography Authors: Woo, L.W.L. / Fischer, D.S. / Sharland, C.M. / Trusselle, M. / Foster, P.A. / Chander, S.K. / Di Fiore, A. / Supuran, C.T. / De Simone, G. / Purohit, A. / Reed, M.J. / Potter, B.V.L. #1: Journal: J.Med.Chem. / Year: 2006 Title: 2-substituted estradiol bis-sulfamates, multitargeted antitumor agents: synthesis, in vitro SAR, protein crystallography, and in vivo activity Authors: Leese, M.P. / Leblond, B. / Smith, A. / Newman, S.P. / Di Fiore, A. / De Simone, G. / Supuran, C.T. / Purohit, A. / Reed, M.J. / Potter, B.V. #2: Journal: To be Published Title: Structure Activity Relationships of C-17 Cyano-Substituted Estratrienes as Anticancer Agents Authors: Leese, M.P. / Jourdan, F. / Gaukroger, K. / Mahon, M.F. / Newman, S.P. / Foster, P. / Stengel, C. / Regis-Lydi, S. / Ferrandis, E. / Di Fiore, A. / De Simone, G. / Supuran, C.T. / Purohit, A. ...Authors: Leese, M.P. / Jourdan, F. / Gaukroger, K. / Mahon, M.F. / Newman, S.P. / Foster, P. / Stengel, C. / Regis-Lydi, S. / Ferrandis, E. / Di Fiore, A. / De Simone, G. / Supuran, C.T. / Purohit, A. / Reed, M.J. / Potter, B.V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c7p.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c7p.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 3c7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c7p_validation.pdf.gz | 1022.9 KB | Display | wwPDB validaton report |
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Full document | 3c7p_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3c7p_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 3c7p_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/3c7p ftp://data.pdbj.org/pub/pdb/validation_reports/c7/3c7p | 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, 287 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-POF / ( |
#5: Chemical | ChemComp-MBO / |
#6: Chemical | ChemComp-GOL / |
#7: Water | ChemComp-HOH / |
-Details
Nonpolymer details | THE SYNONYM OF POF IS STX237 |
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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: 2.07 Å3/Da / Density % sol: 40.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 2.6M Ammonium Sulphate, 0.3M Sodium Chloride, 0.1M Tris-HCl pH 8.4, 5mM mercury para-hydroxybenzoate , 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: May 20, 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: 1.7→20 Å / Num. all: 25893 / Num. obs: 25893 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rsym value: 0.074 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 2.7 / Num. unique all: 2430 / Rsym value: 0.344 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1CA2 Resolution: 1.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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