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- PDB-5g01: An unusual natural product primary sulfonamide: synthesis, carbon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5g01 | ||||||
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Title | An unusual natural product primary sulfonamide: synthesis, carbonic anhydrase inhibition and protein x-ray structure of Psammaplin C | ||||||
![]() | CARBONIC ANHYDRASE 2 | ||||||
![]() | LYASE / NATURAL PRODUCT INHIBITOR / ENGINEERED PROTEINS / CARBONIC ANHYDRASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mujumdar, P. / Supuran, C.T. / Peat, T.S. / Poulsen, S.A. | ||||||
![]() | ![]() Title: An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structures of Psammaplin C. Authors: Mujumdar, P. / Teruya, K. / Tonissen, K.F. / Vullo, D. / Supuran, C.T. / Peat, T.S. / Poulsen, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.1 KB | Display | ![]() |
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PDB format | ![]() | 105.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a6hSC ![]() 5g03C ![]() 5g0bC ![]() 5g0cC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29233.855 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 1-260 / Mutation: YES Source method: isolated from a genetically manipulated source Details: A MIMIC OF CA12 BASED ON THE CA2 SCAFFOLD / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 279 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/OE2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OE2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THE FOLLOWING MUTATIONS WERE MADE TO MAKE A CA12 MIMIC A65S, N67K, E69N, I91T, F131A, G132S, V135S, ...THE FOLLOWING MUTATIONS WERE MADE TO MAKE A CA12 MIMIC A65S, N67K, E69N, I91T, F131A, G132S, V135S, L204N, C206T |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: 200 NL PLUS 200 NL OF PROTEIN AT 5 MGS/ML AND RESERVOIR IN SITTING DROP PLATES. RESERVOIR WAS 2.6 TO 2.8 M AMMONIUM SULFATE WITH 100 MM TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→41.5 Å / Num. obs: 47179 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.2 / % possible all: 84.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5A6H Resolution: 1.4→69.49 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.198 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THERE ARE TWO LIGANDS BOUND AND SOME EXTRA DENSITY THAT WAS NOT MODELLED.
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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 mean: 16.176 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→69.49 Å
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Refine LS restraints |
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