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Yorodumi- PDB-2hnc: Crystal structure of the human carbonic anhydrase II in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hnc | ||||||
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Title | Crystal structure of the human carbonic anhydrase II in complex with the 5-amino-1,3,4-thiadiazole-2-sulfonamide inhibitor. | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Protein-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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å | ||||||
Authors | Menchise, V. / Di Fiore, A. / De Simone, G. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Carbonic anhydrase inhibitors: X-ray crystallographic studies for the binding of 5-amino-1,3,4-thiadiazole-2-sulfonamide and 5-(4-amino-3-chloro-5-fluorophenylsulfonamido)-1,3,4-thiadiazole-2- ...Title: Carbonic anhydrase inhibitors: X-ray crystallographic studies for the binding of 5-amino-1,3,4-thiadiazole-2-sulfonamide and 5-(4-amino-3-chloro-5-fluorophenylsulfonamido)-1,3,4-thiadiazole-2-sulfonamide to human isoform II. Authors: Menchise, V. / De Simone, G. / Di Fiore, A. / Scozzafava, A. / Supuran, C.T. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hnc.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hnc.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hnc_validation.pdf.gz | 752 KB | Display | wwPDB validaton report |
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Full document | 2hnc_full_validation.pdf.gz | 756 KB | Display | |
Data in XML | 2hnc_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 2hnc_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/2hnc ftp://data.pdbj.org/pub/pdb/validation_reports/hn/2hnc | HTTPS FTP |
-Related structure data
Related structure data | 2hocC 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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Details | The biological assembly is a monomer. |
-Components
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 203 molecules
#2: Chemical | ChemComp-ZN / | ||
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#3: Chemical | ChemComp-1SA / | ||
#4: Chemical | ChemComp-MBO / | ||
#5: Chemical | #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: 2.08 Å3/Da / Density % sol: 40.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 2.5 M Ammonium Sulphate, 0.3 M Sodium Chloride, 0.1 M Tris-HCl pH 8.2, 5 mM 4-(hydroxymercurybenzoate)., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. all: 34175 / Num. obs: 34175 / % possible obs: 97.8 % / Rsym value: 0.048 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.55→1.61 Å / Mean I/σ(I) obs: 5.52 / Rsym value: 0.164 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1ca2 Resolution: 1.55→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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