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- PDB-5g03: An unusual natural product primary sulfonamide: synthesis, carbon... -
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Basic information
Entry | Database: PDB / ID: 5g03 | ||||||
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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 / PROTEIN ENGINEERING / 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 | ![]() | 133.6 KB | Display | ![]() |
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PDB format | ![]() | 104 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 820 KB | Display | ![]() |
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Full document | ![]() | 822.3 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a6hSC ![]() 5g01C ![]() 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
#1: Protein | Mass: 29226.859 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 1-260 / Mutation: YES Source method: isolated from a genetically manipulated source Details: CAII PROTEIN MUTATED IN ACTIVE SITE TO MIMIC CAIX PROTEIN Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-OE2 / |
#5: Water | ChemComp-HOH / |
Sequence details | CAII PROTEIN MUTATED TO MIMIC CAIX PROTEIN WITH THE FOLLOWING MUTATIONS A65S, N67Q, E69T, I91L, ...CAII PROTEIN MUTATED TO MIMIC CAIX PROTEIN WITH THE FOLLOWING MUTATIONS A65S, N67Q, E69T, I91L, F131V, G132D, V135L, K170E, L204A, C206G |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.2 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: 150 NL PROTEIN AT 5.5 MG/ML PLUS 120 NL RESERVOIR AND 30 NL SEEDS IN SITTING DROP PLATES. RESERVOIR WAS 2.6 TO 2.8 M AMMONIUM SULFATE PLUS 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: 1.35→41.3 Å / Num. obs: 50188 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.4 / % possible all: 90.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A6H Resolution: 1.35→69.62 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.888 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE INHIBITOR IS MOSTLY DISORDERED BEYOND THE SULFONAMIDE WHICH IS BOUND TO THE ZINC ATOM. THE WHOLE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE INHIBITOR IS MOSTLY DISORDERED BEYOND THE SULFONAMIDE WHICH IS BOUND TO THE ZINC ATOM. THE WHOLE MOLECULE IS MODELLED ALTHOUGH THERE IS LITTLE DENSITY BEYOND THE SECOND CARBON LINKING THE SULFONAMIDE TO THE REST OF THE COMPOUND.
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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: 15.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→69.62 Å
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Refine LS restraints |
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