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Yorodumi- PDB-6faf: Crystal structure of human carbonic anhydrase I in complex with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6faf | ||||||
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Title | Crystal structure of human carbonic anhydrase I in complex with the 3-(2,5-dimethylphenyl)-1-(2-hydroxy-5-sulfamoylphenyl)urea inhibitor | ||||||
Components | Carbonic anhydrase 1 | ||||||
Keywords | LYASE | ||||||
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: 1.99 Å | ||||||
Authors | Ferraroni, M. / Supuran, C.T. / Bozdag, M. / Chiapponi, D. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Discovery of 4-Hydroxy-3-(3-(phenylureido)benzenesulfonamides as SLC-0111 Analogues for the Treatment of Hypoxic Tumors Overexpressing Carbonic Anhydrase IX. Authors: Bozdag, M. / Carta, F. / Ceruso, M. / Ferraroni, M. / McDonald, P.C. / Dedhar, 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 | 6faf.cif.gz | 120.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6faf.ent.gz | 91.1 KB | Display | PDB format |
PDBx/mmJSON format | 6faf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/6faf ftp://data.pdbj.org/pub/pdb/validation_reports/fa/6faf | HTTPS FTP |
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-Related structure data
Related structure data | 6f3bC 6fagC 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
#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 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 28% PEG4000, 0.2 M Sodium acetate, Tris 100 mM |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.973 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.99→61.23 Å / Num. obs: 34911 / % possible obs: 92.9 % / Redundancy: 3.924 % / Biso Wilson estimate: 40.811 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.061 / Χ2: 1.054 / Net I/σ(I): 13.65 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.99→61.23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.589 / SU ML: 0.188 / SU R Cruickshank DPI: 0.2195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.193 / 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: 95.07 Å2 / Biso mean: 42.996 Å2 / Biso min: 22.2 Å2
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Refinement step | Cycle: final / Resolution: 1.99→61.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.993→2.045 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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