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Yorodumi- PDB-6h2z: The crystal structure of human carbonic anhydrase II in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h2z | ||||||
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Title | The crystal structure of human carbonic anhydrase II in complex with 4-(4-phenylpiperidine-1-carbonyl)benzenesulfonamide. | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Protein-inhibitor binding | ||||||
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: 1.94 Å | ||||||
Authors | Buemi, M.R. / Di Fiore, A. / De Luca, L. / Ferro, S. / Mancuso, F. / Monti, S.M. / Buonanno, M. / Angeli, A. / Russo, E. / De Sarro, G. ...Buemi, M.R. / Di Fiore, A. / De Luca, L. / Ferro, S. / Mancuso, F. / Monti, S.M. / Buonanno, M. / Angeli, A. / Russo, E. / De Sarro, G. / Supuran, C.T. / De Simone, G. / Gitto, R. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2018 Title: Exploring structural properties of potent human carbonic anhydrase inhibitors bearing a 4-(cycloalkylamino-1-carbonyl)benzenesulfonamide moiety. Authors: Buemi, M.R. / Di Fiore, A. / De Luca, L. / Angeli, A. / Mancuso, F. / Ferro, S. / Monti, S.M. / Buonanno, M. / Russo, E. / De Sarro, G. / De Simone, G. / Supuran, C.T. / Gitto, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h2z.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h2z.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 6h2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h2z_validation.pdf.gz | 710.8 KB | Display | wwPDB validaton report |
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Full document | 6h2z_full_validation.pdf.gz | 713.4 KB | Display | |
Data in XML | 6h2z_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 6h2z_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/6h2z ftp://data.pdbj.org/pub/pdb/validation_reports/h2/6h2z | HTTPS FTP |
-Related structure data
Related structure data | 6h33C 6h34C 6h36C 6h37C 6h38C 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: 29477.307 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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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-FKE / | ||
#4: Chemical | #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: 2.05 Å3/Da / Density % sol: 40.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: sodium citrate 1.3M, Tris-HCl 0.1 M, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 29, 2018 / Details: MIRROR |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→34.7 Å / Num. obs: 17564 / % possible obs: 98.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.063 / Rrim(I) all: 0.131 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.94→2.01 Å / Rmerge(I) obs: 0.418 / Num. unique obs: 1610 / Rpim(I) all: 0.336 / Rrim(I) all: 0.57 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1CA2 Resolution: 1.94→34.7 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.94→34.7 Å
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LS refinement shell | Resolution: 1.94→2.01 Å
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