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Yorodumi- PDB-6i0l: Crystal structure of human carbonic anhydrase I in complex with t... -
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-Basic information
Entry | Database: PDB / ID: 6i0l | ||||||
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Title | Crystal structure of human carbonic anhydrase I in complex with the 1-[4-chloro-3-(trifluoromethyl)phenyl]-3-[2-(4-sulfamoylphenyl)ethyl]urea inhibitor | ||||||
Components | Carbonic anhydrase 1 | ||||||
Keywords | LYASE / carbonic anhydrase I / inhibitor | ||||||
Function / homology | Function and homology information hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å | ||||||
Authors | Ferraroni, M. / Supuran, C.T. / Bozdag, M. / Chiapponi, D. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2019 Title: Carbonic anhydrase inhibitors based on sorafenib scaffold: Design, synthesis, crystallographic investigation and effects on primary breast cancer cells. Authors: Bozdag, M. / Ferraroni, M. / Ward, C. / Carta, F. / Bua, S. / Angeli, A. / Langdon, S.P. / Kunkler, I.H. / Al-Tamimi, A.S. / Supuran, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i0l.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i0l.ent.gz | 97 KB | Display | PDB format |
PDBx/mmJSON format | 6i0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/6i0l ftp://data.pdbj.org/pub/pdb/validation_reports/i0/6i0l | HTTPS FTP |
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-Related structure data
Related structure data | 6i0jC 1jv0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28906.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00915, carbonic anhydrase |
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-Non-polymers , 5 types, 512 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / | #6: 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: 2.36 Å3/Da / Density % sol: 47.88 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 28% PEG 4000, 0,2 M Sodium acetate, Tris 100 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 13, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→28.6 Å / Num. obs: 105401 / % possible obs: 98.6 % / Redundancy: 3.46 % / Biso Wilson estimate: 30.016 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.051 / Χ2: 1.138 / Net I/σ(I): 11.88 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1jv0 Resolution: 1.4→28.6 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.772 / SU ML: 0.093 / SU R Cruickshank DPI: 0.0694 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.073 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.88 Å2 / Biso mean: 29.631 Å2 / Biso min: 15.72 Å2
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Refinement step | Cycle: final / Resolution: 1.4→28.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.397→1.433 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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