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Yorodumi- PDB-3t5z: Crystal structure of the human carbonic anhydrase II in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t5z | ||||||
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Title | Crystal structure of the human carbonic anhydrase II in complex with N-methoxy-benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / Protein-inhibitor complex / LYASE-LYASE INHIBITOR complex | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.65 Å | ||||||
Authors | Di Fiore, A. / Maresca, A. / Alterio, V. / Supuran, C.T. / De Simone, G. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2011 Title: Carbonic anhydrase inhibitors: X-ray crystallographic studies for the binding of N-substituted benzenesulfonamides to human isoform II. Authors: Di Fiore, A. / Maresca, A. / Alterio, V. / Supuran, C.T. / De Simone, G. #1: Journal: Proteins / Year: 1988 Title: Refined structure of human carbonic anhydrase II at 2.0 A resolution. Authors: Eriksson, A.E. / Jones, T.A. / Liljas, A. #2: Journal: Chemmedchem / Year: 2009 Title: Thermodynamic optimisation in drug discovery: a case study using carbonic anhydrase inhibitors. Authors: Scott, A.D. / Phillips, C. / Alex, A. / Flocco, M. / Bent, A. / Randall, A. / O'Brien, R. / Damian, L. / Jones, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t5z.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t5z.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 3t5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/3t5z ftp://data.pdbj.org/pub/pdb/validation_reports/t5/3t5z | HTTPS FTP |
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-Related structure data
Related structure data | 3t5uC 1ca2S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 29157.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-B09 / |
#4: Chemical | ChemComp-MBO / |
#5: 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: 2.08 Å3/Da / Density % sol: 40.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.6 M ammonium sulfate, 0.3 M sodium chloride, 0.1 M Tris-HCl, pH 8.5, 5 mM 4-hydroxymercurybenzoate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN / Detector: CCD / Date: Feb 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 28042 / Num. obs: 28042 / % possible obs: 96.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 21.03 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 13.45 / Num. unique all: 2511 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1CA2 Resolution: 1.65→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 43.3279 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 52.48 Å2 / Biso mean: 13.6681 Å2 / Biso min: 2.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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Xplor file |
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