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Yorodumi- PDB-2hd6: Crystal structure of the human carbonic anhydrase II in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hd6 | ||||||
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Title | Crystal structure of the human carbonic anhydrase II in complex with a hypoxia-activatable sulfonamide. | ||||||
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 / 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 / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | De Simone, G. / Vitale, R.M. / Di Fiore, A. / Pedone, C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2006 Title: Carbonic anhydrase inhibitors: Hypoxia-activatable sulfonamides incorporating disulfide bonds that target the tumor-associated isoform IX. Authors: De Simone, G. / Vitale, R.M. / Di Fiore, A. / Pedone, C. / Scozzafava, A. / Montero, J.L. / Winum, J.Y. / 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 | 2hd6.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hd6.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/2hd6 ftp://data.pdbj.org/pub/pdb/validation_reports/hd/2hd6 | HTTPS FTP |
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-Related structure data
Related structure data | 1ca2S 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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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 , 6 types, 235 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-MBO / |
#5: Chemical | ChemComp-BOS / |
#6: Chemical | ChemComp-GOL / |
#7: 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: 2.07 Å3/Da / Density % sol: 40.46 % |
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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: May 20, 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: 1.8→20 Å / Num. obs: 21376 / % possible obs: 96 % / Rsym value: 0.055 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 0.21 / % possible all: 86.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1CA2 Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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