[English] 日本語
Yorodumi- PDB-3hlj: Crystal structure of human carbonic anhydrase isozyme II with 3-m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hlj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human carbonic anhydrase isozyme II with 3-methylthiobenzimidazo[1,2-c][1,2,3]thiadiazol-7-sulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / drug design / carbonic anhydrase / sulfonamide / thiadiazole / 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 / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å | ||||||
Authors | Grazulis, S. / Manakova, E. / Golovenko, D. | ||||||
Citation | Journal: J Enzyme Inhib Med Chem / Year: 2010 Title: Inhibition and binding studies of carbonic anhydrase isozymes I, II and IX with benzimidazo[1,2-c][1,2,3]thiadiazole-7-sulphonamides Authors: Baranauskiene, L. / Hilvo, M. / Matuliene, J. / Golovenko, D. / Manakova, E. / Dudutiene, V. / Michailoviene, V. / Torresan, J. / Jachno, J. / Parkkila, S. / Maresca, A. / Supuran, C.T. / ...Authors: Baranauskiene, L. / Hilvo, M. / Matuliene, J. / Golovenko, D. / Manakova, E. / Dudutiene, V. / Michailoviene, V. / Torresan, J. / Jachno, J. / Parkkila, S. / Maresca, A. / Supuran, C.T. / Grazulis, S. / Matulis, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3hlj.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3hlj.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 3hlj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/3hlj ftp://data.pdbj.org/pub/pdb/validation_reports/hl/3hlj | HTTPS FTP |
---|
-Related structure data
Related structure data | 2nnsS 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: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase |
---|
-Non-polymers , 5 types, 230 molecules
#2: Chemical | ChemComp-V21 / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | ChemComp-UNX / #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THE NUMBER 126 IS SIMPLY SKIPPED IN THE ENTRY TO KEEP THE ACTIVE CENTER RESIDUES NUMBERING BETWEEN ...THE NUMBER 126 IS SIMPLY SKIPPED IN THE ENTRY TO KEEP THE ACTIVE CENTER RESIDUES NUMBERING BETWEEN DIFFERENT CARBONIC ANHYDRASE ISOFORMS CONSISTENT |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40.5 % / Mosaicity: 0.848 ° |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Crystallization buffer was 0.1M sodium BICINE, pH9.0, 0.2M ammonium sulfate and 2M sodium malonate, pH7.0 made from 1M sodium BICINE and 3.4M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 27, 2007 / Details: mirrors |
Radiation | Monochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 1.438→24.456 Å / Num. all: 42194 / Num. obs: 42194 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 7.015 |
Reflection shell | Resolution: 1.44→1.52 Å / Redundancy: 4 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.7 / Num. measured all: 22437 / Num. unique all: 5634 / Rsym value: 0.431 / % possible all: 89.3 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NNS Resolution: 1.44→23.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.173 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.882 / SU B: 2.739 / SU ML: 0.048 / SU R Cruickshank DPI: 0.096 / SU Rfree: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.096 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; As for the UNK residue, it looks like it is a part of the MES molecule. There is only the ring, which is visible in the structure but -CH2- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; As for the UNK residue, it looks like it is a part of the MES molecule. There is only the ring, which is visible in the structure but -CH2-CH2-SO3 moiety is not fixed. So the depositors have decided to remove this moiety from the MES molecule, because at any rate they are not able to say anything reasonable about its orientation.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.7 Å2 / Biso mean: 16.481 Å2 / Biso min: 5.81 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→23.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.441→1.479 Å / Total num. of bins used: 20
|