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Yorodumi- PDB-5u0e: Identification of a New Zinc Binding Chemotype by Fragment Screening -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u0e | ||||||
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Title | Identification of a New Zinc Binding Chemotype by Fragment Screening | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Fragment screening / 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 / 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: 1.27 Å | ||||||
Authors | Peat, T.S. / Poulsen, S.A. / Ren, B. / Dolezal, O. / Woods, L.A. / Mujumdar, P. / Chrysanthopoulos, P.K. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Identification of a New Zinc Binding Chemotype by Fragment Screening. Authors: Chrysanthopoulos, P.K. / Mujumdar, P. / Woods, L.A. / Dolezal, O. / Ren, B. / Peat, T.S. / Poulsen, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u0e.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u0e.ent.gz | 108.3 KB | Display | PDB format |
PDBx/mmJSON format | 5u0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/5u0e ftp://data.pdbj.org/pub/pdb/validation_reports/u0/5u0e | HTTPS FTP |
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-Related structure data
Related structure data | 5txyC 5ty1C 5ty8C 5ty9C 5tyaC 5u0dC 5u0fC 5u0gC 5vgyC 4cq0S 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: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 315 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-7R4 / ( |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.58 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals ...Details: the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals several days before harvesting and data collection |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→41.5 Å / Num. obs: 63095 / % possible obs: 96.1 % / Redundancy: 7.3 % / CC1/2: 0.999 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.26→1.28 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.2 / CC1/2: 0.702 / % possible all: 65.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4cq0 Resolution: 1.27→41.5 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.531 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.04 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.068 Å2
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Refinement step | Cycle: 1 / Resolution: 1.27→41.5 Å
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Refine LS restraints |
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