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Yorodumi- PDB-6g3v: Crystal structure of human carbonic anhydrase I in complex with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g3v | ||||||
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Title | Crystal structure of human carbonic anhydrase I in complex with the inhibitor famotidine | ||||||
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: 1.69 Å | ||||||
Authors | Ferraroni, M. / Supuran, C.T. / Angeli, A. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2018 Title: Famotidine, an Antiulcer Agent, Strongly InhibitsHelicobacter pyloriand Human Carbonic Anhydrases. Authors: Angeli, A. / Ferraroni, M. / 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 | 6g3v.cif.gz | 117.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g3v.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 6g3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/6g3v ftp://data.pdbj.org/pub/pdb/validation_reports/g3/6g3v | HTTPS FTP |
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-Related structure data
Related structure data | 6g3qC 3lxeS 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 / Details: erytrocytes / Source: (natural) Homo sapiens (human) / References: UniProt: P00915, carbonic anhydrase #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / 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: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→30 Å / Num. all: 158183 / Num. obs: 57352 / % possible obs: 93.5 % / Redundancy: 2.75 % / CC1/2: 0.99 / Rrim(I) all: 0.083 / Rsym value: 0.068 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.69→1.8 Å / Redundancy: 2.2 % / Num. unique obs: 8041 / CC1/2: 0.37 / Rrim(I) all: 0.151 / Rsym value: 0.12 / % possible all: 82.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3LXE Resolution: 1.69→27 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.37 / SU ML: 0.128 / SU R Cruickshank DPI: 0.1275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.13 / 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: 114.34 Å2 / Biso mean: 30.799 Å2 / Biso min: 14.93 Å2
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Refinement step | Cycle: final / Resolution: 1.69→27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.693→1.737 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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