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Yorodumi- PDB-3po6: Crystal structure of human carbonic anhydrase II with 6,7-Dimetho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3po6 | ||||||
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Title | Crystal structure of human carbonic anhydrase II with 6,7-Dimethoxy-1-methyl-3,4-dihydroisoquinoline-2(1H)-sulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / Carbonic anhydrase / 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 / 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: 1.47 Å | ||||||
Authors | Mader, P. / Brynda, J. / Gitto, R. / Agnello, S. / Ferro, S. / De Luca, L. / Vullo, D. / Supuran, C.T. / Chimirri, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Structural basis for the interaction between carbonic anhydrase and 1,2,3,4-tetrahydroisoquinolin-2-ylsulfonamides. Authors: Mader, P. / Brynda, J. / Gitto, R. / Agnello, S. / Pachl, P. / Supuran, C.T. / Chimirri, A. / Rezacova, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3po6.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3po6.ent.gz | 104.1 KB | Display | PDB format |
PDBx/mmJSON format | 3po6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/3po6 ftp://data.pdbj.org/pub/pdb/validation_reports/po/3po6 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 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, 321 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-DT9 / ( | ||||
#4: Chemical | ChemComp-RDT / ( | ||||
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | RESIDUE NUMBER 126 IS SIMPLY SKIPPED. |
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-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: 40.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.1M Tris-Cl, 2.5M ammonium sulfate, 0.3M sodium chloride, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9537 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→26.62 Å / Num. all: 40809 / Num. obs: 39222 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 13.74 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 7.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.47→25.27 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.227 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.023 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→25.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.472→1.51 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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