[English] 日本語
Yorodumi- PDB-2hl4: Crystal structure analysis of human carbonic anhydrase II in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hl4 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure analysis of human carbonic anhydrase II in complex with a benzenesulfonamide derivative | |||||||||
Components | Carbonic anhydrase 2 | |||||||||
Keywords | LYASE / Protein-inhibitor complex | |||||||||
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: 1.55 Å | |||||||||
Authors | Di Fiore, A. / Supuran, C.T. / Winum, J.-Y. / Montero, J.-L. / Pedone, C. / Scozzafava, A. / De Simone, G. | |||||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: Carbonic anhydrase inhibitors: binding of an antiglaucoma glycosyl-sulfanilamide derivative to human isoform II and its consequences for the drug design of enzyme inhibitors incorporating sugar moieties Authors: Di Fiore, A. / Scozzafava, A. / Winum, J.-Y. / Montero, J.-L. / Pedone, C. / Supuran, C.T. / De Simone, G. #1: Journal: Proteins / Year: 1988 Title: Refined structure of human carbonic anhydrase II at 2.0 A resolution Authors: Eriksson, A.E. / Jones, T.A. / Liljas, A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2hl4.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2hl4.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 2hl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/2hl4 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/2hl4 | 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 / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 29157.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sigma-Aldrich Co. / Source: (natural) Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase |
---|---|
#4: Sugar | ChemComp-BO1 / |
-Non-polymers , 5 types, 325 molecules
#2: Chemical | ChemComp-ZN / |
---|---|
#3: Chemical | ChemComp-CL / |
#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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 2.5M Ammonium Sulphate, 0.3M Sodium Chloride, 0.1M Tris-HCl, 5mM mercury-parahydroxybenzoate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 19, 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: 1.55→20 Å / Num. all: 34882 / Num. obs: 34301 / % possible obs: 99.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3304 / % possible all: 96.7 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1CA2 Resolution: 1.55→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Displacement parameters | Biso mean: 12.72 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
| ||||||||||||||||||||
Refine LS restraints |
|