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Yorodumi- PDB-4k0z: Structure of HCAIX mimic (HCAII with 5 mutations in active site) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k0z | ||||||
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Title | Structure of HCAIX mimic (HCAII with 5 mutations in active site) in complex with methazolamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / alpha beta fold | ||||||
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 / regulation of intracellular pH / morphogenesis of an epithelium / 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: 1.799 Å | ||||||
Authors | Biswas, S. / McKenna, R. | ||||||
Citation | Journal: To be Published Title: Developing isoform specific inhibitors for hCAIX using CAIX mimic Authors: Biswas, S. / West, D. / Pinard, M. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k0z.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k0z.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 4k0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/4k0z ftp://data.pdbj.org/pub/pdb/validation_reports/k0/4k0z | HTTPS FTP |
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-Related structure data
Related structure data | 4k13C 4k1qC 2iliS 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: 29038.719 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, E69T, F131L, K170E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-MZM / | #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: 2.04 Å3/Da / Density % sol: 39.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6 M sodium citrate, 50 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 9, 2011 |
Radiation | Monochromator: varimax optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→50 Å / Num. all: 22787 / Num. obs: 22787 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.799→1.86 Å / Redundancy: 6 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 6.9 / Rsym value: 0.265 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ILI Resolution: 1.799→33.821 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 15.75 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.799→33.821 Å
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Refine LS restraints |
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LS refinement shell |
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