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Yorodumi- PDB-5g0c: An unusual natural product primary sulfonamide: synthesis, carbon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g0c | ||||||
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Title | An unusual natural product primary sulfonamide: synthesis, carbonic anhydrase inhibition and protein x-ray structure of Psammaplin C | ||||||
Components | CARBONIC ANHYDRASE 2 | ||||||
Keywords | LYASE / PROTEIN ENGINEERING / NATURAL PRODUCT INHIBITOR / CARBONIC ANHYDRASE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Mujumdar, P. / Supuran, C.T. / Peat, T.S. / Poulsen, S.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g0c.cif.gz | 139.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g0c.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 5g0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g0c_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 5g0c_full_validation.pdf.gz | 445.5 KB | Display | |
Data in XML | 5g0c_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 5g0c_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/5g0c ftp://data.pdbj.org/pub/pdb/validation_reports/g0/5g0c | HTTPS FTP |
-Related structure data
Related structure data | 5a6hSC 5g01C 5g03C 5g0bC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: CAII BACKBONE AND MUTATIONS IN THE ACTIVE SITE TO MAKE IT A CAIX MIMIC Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 332 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | CAII BACKBONE AND MUTATIONS IN THE ACTIVE SITE INTRODUCED TO MAKE IT A CAXII MIMIC, WITH THE ...CAII BACKBONE AND MUTATIONS IN THE ACTIVE SITE INTRODUCED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.9 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: SITTING DROP PLATES WITH 200 NL PROTEIN AT 5 MG/ML AND 200 NL RESERVOIR WITH 2.6 TO 2.8 M AMMONIUM SULFATE AND 100 MM TRIS AT PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 |
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: 1.28→41.3 Å / Num. obs: 59861 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.28→1.3 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.3 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A6H Resolution: 1.28→69.5 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.65 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 13.377 Å2
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Refinement step | Cycle: LAST / Resolution: 1.28→69.5 Å
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Refine LS restraints |
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