[English] 日本語
Yorodumi- PDB-7o48: Crystal structure of carbonic anhydrase from schistosoma mansoni ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o48 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of carbonic anhydrase from schistosoma mansoni with 4-(2-(3-(4-iodophenyl)thioureido)ethyl)benzenesulfonamide | ||||||
Components | Carbonic anhydrase | ||||||
Keywords | LYASE / schistosoma mansoni / carbonic anhydrase / sulfonamide | ||||||
Function / homology | Function and homology information carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / zinc ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Schistosoma mansoni (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Angeli, A. / Ferraroni, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structural Insights into Schistosoma mansoni Carbonic Anhydrase (SmCA) Inhibition by Selenoureido-Substituted Benzenesulfonamides. Authors: Angeli, A. / Ferraroni, M. / Da'dara, A.A. / Selleri, S. / Pinteala, M. / Carta, F. / Skelly, P.J. / Supuran, C.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7o48.cif.gz | 141.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7o48.ent.gz | 108 KB | Display | PDB format |
PDBx/mmJSON format | 7o48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/7o48 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/7o48 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6qqmSC 7bfaC 7bg5C 7bhhC 7bm4C 7nexC 7ng1C 7nwyC 7o2sC 7oa1C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35704.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q0KSG2, carbonic anhydrase |
---|
-Sugars , 2 types, 5 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 367 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.35 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 20% PEG 6000, 0.1 M citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9999 / Wavelength: 1 Å | |||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2020 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.81→30 Å / Num. obs: 76567 / % possible obs: 99.3 % / Redundancy: 16.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.091 / Net I/σ(I): 19.58 | |||||||||
Reflection shell | Resolution: 1.81→1.84 Å / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 5627 / CC1/2: 0.862 / Rrim(I) all: 0.801 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6qqm Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.954 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.39 Å2 / Biso mean: 31.029 Å2 / Biso min: 15.71 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|