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Yorodumi- PDB-3mhl: Crystal structure of human carbonic anhydrase isozyme II with 4-{... -
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-Basic information
Entry | Database: PDB / ID: 3mhl | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme II with 4-{[N-(6-methoxy-5-nitropyrimidin-4-yl)amino]methyl}benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / sulfonamide / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 | 3mhl.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mhl.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mhl_validation.pdf.gz | 737.8 KB | Display | wwPDB validaton report |
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Full document | 3mhl_full_validation.pdf.gz | 739.4 KB | Display | |
Data in XML | 3mhl_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3mhl_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/3mhl ftp://data.pdbj.org/pub/pdb/validation_reports/mh/3mhl | HTTPS FTP |
-Related structure data
Related structure data | 3m3xC 3m40C 3m5eC 3mhiC 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 | #4: Chemical | ChemComp-J71 / | #5: Water | ChemComp-HOH / | Nonpolymer details | METAL ION NATURALLY OCCURS IN CARBONIC ANHYDRASES | Sequence 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: 1.99 Å3/Da / Density % sol: 38.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 9 Details: 0.1M Na-bicine pH 9, 2.6M Na-malonate pH 7, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.972 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2009 / Details: Vertically focussing mirror |
Radiation | Monochromator: Double crystal Si(111), horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40.689 Å / Num. all: 18388 / Num. obs: 18388 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 37.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 7.5 / Num. measured all: 30321 / Num. unique all: 2642 / Rsym value: 0.252 / % possible all: 100 |
-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: 1.9→40.46 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.159 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.861 / SU B: 3.489 / SU ML: 0.104 / SU R Cruickshank DPI: 0.17 / SU Rfree: 0.157 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17 / ESU R Free: 0.157 / 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: 66.5 Å2 / Biso mean: 25.533 Å2 / Biso min: 10.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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