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- PDB-5a6h: Synthesis, carbonic anhydrase inhibition and protein X-ray struct... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a6h | ||||||
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Title | Synthesis, carbonic anhydrase inhibition and protein X-ray structure of the unusual natural product primary sulfonamide Psammaplin C | ||||||
![]() | CARBONIC ANHYDRASE 2 | ||||||
![]() | LYASE / CARBONIC ANHYDRASE INHIBITOR / NATURAL PRODUCT | ||||||
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. | ||||||
![]() | ![]() 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 | ![]() | 124.5 KB | Display | ![]() |
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PDB format | ![]() | 96.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g01C ![]() 5g03C ![]() 5g0bC ![]() 5g0cC ![]() 4cq0S S: Starting model for refinement C: citing same article ( |
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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: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | ChemComp-DMS / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | PSAMMAPLIN | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.8 % / Description: NONE |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion / pH: 8 Details: EQUAL VOLUMES OF PROTEIN AND RESERVOIR (250 NL EACH) AT 8C WITH THE PROTEIN AT 7.5 MG/ML AND THE RESERVOIR BEING 2.6 M AMMONIUM SULFATE, 100 MM TRIS PH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 2, 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: 1.57→41.4 Å / Num. obs: 33092 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.8 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4CQ0 Resolution: 1.57→70.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.917 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED THERE IS AT LEAST ONE BLOB OF DENSITY WHICH HAS BEEN LEFT WITHOUT WATER OR OTHER MOLECULE, IN ADDITION THERE IS A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED THERE IS AT LEAST ONE BLOB OF DENSITY WHICH HAS BEEN LEFT WITHOUT WATER OR OTHER MOLECULE, IN ADDITION THERE IS A STRING OF WATER MOLECULES THAT MAY BE SOMETHING BUT NOTHING FROM THE CRYSTALLIZATION CONDITIONS.
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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: 16.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→70.1 Å
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Refine LS restraints |
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