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- PDB-6y00: crystal structure of human carbonic anhydrase I in complex with 4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y00 | ||||||
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Title | crystal structure of human carbonic anhydrase I in complex with 4-(3-(2-((2-fluorobenzyl)amino)ethyl)ureido) benzenesulfonamide | ||||||
![]() | Carbonic anhydrase 1 | ||||||
![]() | LYASE / Inhibitor / carbon dioxide / carbonic anhydrase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zanotti, G. / Majid, A. / Bozdag, M. / Angeli, A. / Carta, F. / Berto, P. / Supuran, C. | ||||||
![]() | ![]() Title: Benzylaminoethyureido-Tailed Benzenesulfonamides: Design, Synthesis, Kinetic and X-ray Investigations on Human Carbonic Anhydrases. Authors: Ali, M. / Bozdag, M. / Farooq, U. / Angeli, A. / Carta, F. / Berto, P. / Zanotti, G. / Supuran, C.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.5 KB | Display | ![]() |
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PDB format | ![]() | 100.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6xzeSC ![]() 6xzoC ![]() 6xzsC ![]() 6xzxC ![]() 6xzyC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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) ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 200 mM Na-acetate, 30% PEG 4000, 100 mM Tris-HCl pH 9. Inhibitor: 150 mM NaCl, 10% DMSO, 50 mM Tris pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→61.5 Å / Num. obs: 114640 / % possible obs: 99.9 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.37→1.41 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1 / Num. unique obs: 8252 / Rpim(I) all: 0.522 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6xze Resolution: 1.37→60.699 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 28.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.33 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→60.699 Å
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Refine LS restraints |
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