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- PDB-3dc9: Use of Carbonic Anhydrase II, IX Active-Site Mimic, for the Purpo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dc9 | ||||||
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Title | Use of Carbonic Anhydrase II, IX Active-Site Mimic, for the Purpose of Screening Inhibitors for Possible Anti-Cancer Properties | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE / Carbonic anhydrase II complex / CAIX mimic inhibitors / Acetylation / Cytoplasm / Disease mutation / Metal-binding / Polymorphism / Zinc | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Genis, C. / Sippel, K.H. / Case, N. / Govindasamy, L. / Agbandje-Mckenna, M. / Mckenna, R. | ||||||
![]() | ![]() Title: Design of a carbonic anhydrase IX active-site mimic to screen inhibitors for possible anticancer properties Authors: Genis, C. / Sippel, K.H. / Case, N. / Cao, W. / Avvaru, B.S. / Tartaglia, L.J. / Govindasamy, L. / Tu, C. / Agbandje-McKenna, M. / Silverman, D.N. / Rosser, C.J. / McKenna, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.9 KB | Display | ![]() |
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PDB format | ![]() | 49.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418 KB | Display | ![]() |
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Full document | ![]() | 420 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3d8wC ![]() 3d9zC ![]() 3dazC ![]() 3dbuC ![]() 3dc3C ![]() 3dccC ![]() 3dcsC ![]() 3dcwC ![]() 3dd0C ![]() 1mooS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29319.086 Da / Num. of mol.: 1 / Mutation: A65S,N67Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.3M sodium citrate, 100mM Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: osmic mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 31389 / Num. obs: 31389 / % possible obs: 94.9 % / Redundancy: 3 % / Rsym value: 0.074 |
Reflection shell | Resolution: 1.6→1.66 Å / Num. unique all: 3000 / Rsym value: 0.279 / % possible all: 91.4 |
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Processing
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Refinement | Method to determine structure: AB INITIO Starting model: PDB entry 1MOO Resolution: 1.6→19.03 Å / Num. parameters: 9087 / Num. restraintsaints: 8699 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2202 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→19.03 Å
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Refine LS restraints |
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