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Yorodumi- PDB-5ll8: Human Carbonic Anhydrase II in complex with aliphatic Benzenesulf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ll8 | ||||||
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Title | Human Carbonic Anhydrase II in complex with aliphatic Benzenesulfonamide inhibitor. | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / PROTEIN-LIGAND-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 / MOLECULAR REPLACEMENT / Resolution: 1.03 Å | ||||||
Authors | Gloeckner, S. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To Be Published Title: Crystallographic, kinetic and thermodynamic characterization of aliphatic Benzenesulfonamides as Ligands of human Carbonic Anhydrase II Authors: Gloeckner, S. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ll8.cif.gz | 177.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ll8.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ll8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/5ll8 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/5ll8 | HTTPS FTP |
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-Related structure data
Related structure data | 3ks3S 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: 29806.588 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The first residues are from a residual expression tag (GSPEF) Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: PGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 6 types, 286 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-6YP / | #5: Chemical | ChemComp-BE7 / ( | #6: Chemical | ChemComp-HG / | #7: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 2.0 uL of protein solution (10.5 mg/mL in 50 mM Tris pH=7.8) were mixed with 2.0 uL of the well solution (2.7 M (NH4)2SO4, 100 mM Tris, pH=7.8, saturated with PCMB) and placed as hanging ...Details: 2.0 uL of protein solution (10.5 mg/mL in 50 mM Tris pH=7.8) were mixed with 2.0 uL of the well solution (2.7 M (NH4)2SO4, 100 mM Tris, pH=7.8, saturated with PCMB) and placed as hanging drop. Crystals appeared after several days. The crystals were soaked in 3.0 M (NH4)2SO4, 100 mM Tris, pH=7.8, saturated with inhibitor) for 1 day. |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 6, 2015 |
Radiation | Monochromator: Si(111) double-crystal fixed-exit monochromator, in the parallel nondispersive mode Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→41.45 Å / Num. obs: 114562 / % possible obs: 95.8 % / Redundancy: 3.8 % / Rsym value: 0.051 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.03→1.09 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.3 / % possible all: 75.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 1.03→40.984 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.03→40.984 Å
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Refine LS restraints |
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LS refinement shell |
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