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Yorodumi- PDB-6xzo: Crystal structure of human carbonic anhydrase I in complex with 4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xzo | ||||||
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Title | Crystal structure of human carbonic anhydrase I in complex with 4-(3-(2-((4-bromo-2-hydroxybenzyl)amino)ethyl)ureido) benzenesulfonamide | ||||||
Components | Carbonic anhydrase 1 | ||||||
Keywords | LYASE / Inhibitor / carbon dioxide / carbonic anhydrase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | ||||||
Authors | Zanotti, G. / Majid, A. / Bozdag, M. / Angeli, A. / Carta, F. / Berto, P. / Supuran, C. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xzo.cif.gz | 136.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xzo.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 6xzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/6xzo ftp://data.pdbj.org/pub/pdb/validation_reports/xz/6xzo | HTTPS FTP |
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-Related structure data
Related structure data | 6xzeSC 6xzsC 6xzxC 6xzyC 6y00C 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) / Plasmid details: erythrocytes / References: UniProt: P00915, carbonic anhydrase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.31 Å3/Da / Density % sol: 46.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop 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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
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: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→61.22 Å / Num. obs: 97700 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.043 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.44→1.48 Å / Redundancy: 12.4 % / Rmerge(I) obs: 2.45 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7186 / Rpim(I) all: 0.735 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6xze Resolution: 1.44→55.28 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / Phase error: 22.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.22 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→55.28 Å
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Refine LS restraints |
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