[English] 日本語
Yorodumi- PDB-2qp6: The crystal structure of the complex of hcaII with a bioreductive... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qp6 | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of the complex of hcaII with a bioreductive antitumor derivative | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / CARBONIC ANHYDRASE II | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å | ||||||
Authors | D'Ambrosio, K. / De Simone, G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Carbonic Anhydrase Inhibitors: Bioreductive Nitro-Containing Sulfonamides with Selectivity for Targeting the Tumor Associated Isoforms IX and XII. Authors: D'Ambrosio, K. / Vitale, R.M. / Dogne, J.M. / Masereel, B. / Innocenti, A. / Scozzafava, A. / De Simone, G. / Supuran, C.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qp6.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qp6.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 2qp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/2qp6 ftp://data.pdbj.org/pub/pdb/validation_reports/qp/2qp6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ca2S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29157.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ERYTHROCYTES / Source: (natural) Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase |
---|
-Non-polymers , 6 types, 362 molecules
#2: Chemical | ChemComp-ZN / |
---|---|
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-HG / |
#5: Chemical | ChemComp-MBO / |
#6: Chemical | ChemComp-MB1 / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.62 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: AMMONIUM SULPHATE, SODIUM CHLORIDE, TRIS-HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277 K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 10, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→20 Å / Num. all: 118328 / Num. obs: 41454 / % possible obs: 97.3 % / Rsym value: 0.045 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.45→1.5 Å / Mean I/σ(I) obs: 4.1 / Num. unique all: 3273 / Rsym value: 0.211 / % possible all: 77.2 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1CA2 Resolution: 1.45→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.45→1.46 Å
|