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Yorodumi- PDB-3v7x: Complex of human carbonic anhydrase II with N-[2-(3,4-dimethoxyph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v7x | ||||||
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Title | Complex of human carbonic anhydrase II with N-[2-(3,4-dimethoxyphenyl)ethyl]-4-sulfamoylbenzamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.03 Å | ||||||
Authors | Mader, P. / Brynda, J. / Rezacova, P. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Synthesis, Structure-Activity Relationship Studies, and X-ray Crystallographic Analysis of Arylsulfonamides as Potent Carbonic Anhydrase Inhibitors. Authors: Gitto, R. / Damiano, F.M. / Mader, P. / De Luca, L. / Ferro, S. / Supuran, C.T. / Vullo, D. / Brynda, J. / Rezacova, P. / Chimirri, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v7x.cif.gz | 144.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v7x.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 3v7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v7x_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3v7x_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3v7x_validation.xml.gz | 19 KB | Display | |
Data in CIF | 3v7x_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/3v7x ftp://data.pdbj.org/pub/pdb/validation_reports/v7/3v7x | HTTPS FTP |
-Related structure data
Related structure data | 3vbdC 3po6S C: citing same article (ref.) 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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-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, 358 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-D7A / | ||||
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MBO / #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: 2.09 Å3/Da / Density % sol: 41.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3 M ammonium sulfate, 50 mM Tris-HCl, 2 mM 4-(Hydroxymercuri)benzoate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 1, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→15.47 Å / Num. all: 118233 / Num. obs: 117997 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.03→1.06 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.584 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3PO6 Resolution: 1.03→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.03→10 Å
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Refine LS restraints |
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