+Open data
-Basic information
Entry | Database: PDB / ID: 8dj9 | ||||||
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Title | Carbonic Anhydrase II in complex with Ibuprofen | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | METAL BINDING PROTEIN / Lyase / Carbonic Anhydrase / Ibuprofen inhibitor | ||||||
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: 1.54 Å | ||||||
Authors | Combs, J.C. / McKenna, R. / Andring, J.T. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2022 Title: Ibuprofen: a weak inhibitor of Carbonic Anhydrase II Authors: Combs, J.C. / Andring, J.T. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dj9.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dj9.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 8dj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/8dj9 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/8dj9 | 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 | Similarity search - Function & homologyF&H Search |
-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: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 333 molecules
#2: Chemical | #3: Chemical | ChemComp-IZP / ( | #4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.15 Å3/Da / Density % sol: 42.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M Sodium Citrate, 50 mM Tris base pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→35.9 Å / Num. obs: 35625 / % possible obs: 96.79 % / Redundancy: 3.4 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.854 / Rmerge(I) obs: 0.2549 / Rpim(I) all: 0.1591 / Rrim(I) all: 0.3014 / Net I/σ(I): 18.56 |
Reflection shell | Resolution: 1.54→1.595 Å / Rmerge(I) obs: 0.4391 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 3017 / CC1/2: 0.911 / Rpim(I) all: 0.3146 / Rrim(I) all: 0.5443 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ks3 Resolution: 1.54→35.84 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.7 Å2 / Biso mean: 17.9474 Å2 / Biso min: 4.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.54→35.84 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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