[English] 日本語
Yorodumi- PDB-6c7x: Carbonic anhydrase 2 in complex with 2-chloro-5'-O-sulfamoyladenosine -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c7x | ||||||
---|---|---|---|---|---|---|---|
Title | Carbonic anhydrase 2 in complex with 2-chloro-5'-O-sulfamoyladenosine | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/INHIBITOR / human carbonic anhydrase II / inhibitor / natural product / LYASE / LYASE-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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Peat, T.S. / Mujumdar, P. / Poulsen, S.A. | ||||||
Citation | Journal: Bioorg. Med. Chem. Lett. / Year: 2018 Title: Synthesis, structure and bioactivity of primary sulfamate-containing natural products. Authors: Mujumdar, P. / Bua, S. / Supuran, C.T. / Peat, T.S. / Poulsen, S.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6c7x.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6c7x.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 6c7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/6c7x ftp://data.pdbj.org/pub/pdb/validation_reports/c7/6c7x | HTTPS FTP |
---|
-Related structure data
Related structure data | 6c7wC 5eh5S 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: pACA / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-EO7 / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.37 % |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Protein was at 10 mg/mL and was set up in 250 plus 250 nL drops with a reservoir of 50 mM Tris pH 8.0, 2.8 M ammonium sulfate at 8C |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9501 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9501 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→41.4 Å / Num. obs: 38990 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.034 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1821 / CC1/2: 0.731 / Rpim(I) all: 0.327 / % possible all: 94.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5eh5 Resolution: 1.5→41.4 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.33 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.567 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.5→41.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|