[English] 日本語
Yorodumi- PDB-6yqt: CRYSTAL STRUCTURE OF HUMAN CA II IN COMPLEX WITH A SULFONAMIDE DE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yqt | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF HUMAN CA II IN COMPLEX WITH A SULFONAMIDE DERIVATIVE OF 2-MERCAPTOBENZOXAZOLE | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / 2-mercaptobenzoxazole-5-sulfonamide / carbonic anhydrase / 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 / morphogenesis of an epithelium / regulation of intracellular pH / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Alterio, V. / De Simone, G. / Esposito, D. | ||||||
Funding support | Italy, 1items
| ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2020 Title: 2-Mercaptobenzoxazoles: a class of carbonic anhydrase inhibitors with a novel binding mode to the enzyme active site. Authors: Bozdag, M. / Supuran, C.T. / Esposito, D. / Angeli, A. / Carta, F. / Monti, S.M. / De Simone, G. / Alterio, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6yqt.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6yqt.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 6yqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yqt_validation.pdf.gz | 913.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6yqt_full_validation.pdf.gz | 914.2 KB | Display | |
Data in XML | 6yqt_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6yqt_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/6yqt ftp://data.pdbj.org/pub/pdb/validation_reports/yq/6yqt | HTTPS FTP |
-Related structure data
Related structure data | 6yquC 6equS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#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: pETM13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-ZN / | ||||||
#3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.3 M sodium citrate, 100 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 21, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→35.67 Å / Num. obs: 38111 / % possible obs: 97.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.029 / Rrim(I) all: 0.07 / Χ2: 1.047 / Net I/av σ(I): 19.9 / Net I/σ(I): 21.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6EQU Resolution: 1.5→35.67 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 41.4328 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 39.12 Å2 / Biso mean: 12.7325 Å2 / Biso min: 3.53 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→35.67 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
|