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Yorodumi- PDB-3m40: Crystal structure of human carbonic anhydrase isozyme II with 4-[... -
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-Basic information
Entry | Database: PDB / ID: 3m40 | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme II with 4-[N-(6-chloro-5-nitropyrimidin-4-yl)amino]benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / DRUG DESIGN / CARBONIC ANHYDRASE / SULFONAMIDE / METAL-BINDING / 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 / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / 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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Grazulis, S. / Manakova, E. / Golovenko, D. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2010 Title: 4-[N-(Substituted 4-pyrimidinyl)amino]benzenesulfonamides as inhibitors of carbonic anhydrase isozymes I, II, VII, and XIII Authors: Sudzius, J. / Baranauskiene, L. / Golovenko, D. / Matuliene, J. / Michailoviene, V. / Torresan, J. / Jachno, J. / Sukackaite, R. / Manakova, E. / Grazulis, S. / Tumkevicius, S. / Matulis, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m40.cif.gz | 131.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m40.ent.gz | 100.7 KB | Display | PDB format |
PDBx/mmJSON format | 3m40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m40_validation.pdf.gz | 749.3 KB | Display | wwPDB validaton report |
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Full document | 3m40_full_validation.pdf.gz | 752.4 KB | Display | |
Data in XML | 3m40_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3m40_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/3m40 ftp://data.pdbj.org/pub/pdb/validation_reports/m4/3m40 | HTTPS FTP |
-Related structure data
Related structure data | 3m3xC 3m5eC 3mhiC 3mhlC 3mhmC 3mhoC 2nnoS 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
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-J45 / | ||
#4: Chemical | ChemComp-DMS / | ||
#5: Water | ChemComp-HOH / | ||
Nonpolymer details | METAL ION NATURALLY OCCURS IN CARBONIC ANHYDRASESSequence details | 126 IS SKIPPED IN THE NUMBERING. | |
-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: 40.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Na-bicine pH 9.0, 2M Na-Malonate pH7.55, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 Å |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 7, 2008 / Details: Bent, vertically focussing mirror |
Radiation | Monochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.815 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→16.295 Å / Num. all: 31929 / Num. obs: 30141 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 12.747 Å2 / Rmerge(I) obs: 0.161 / Rsym value: 0.161 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 6.4 / Num. measured all: 24834 / Num. unique all: 4203 / Rsym value: 0.202 / % possible all: 90.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NNO Resolution: 1.6→14.38 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 3.471 / SU ML: 0.057 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.173 / ESU R Free: 0.113 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.38 Å2 / Biso mean: 13.991 Å2 / Biso min: 3.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→14.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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