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Yorodumi- PDB-5llp: Crystal structure of human carbonic anhydrase isozyme XII with 3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5llp | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme XII with 3-[(1S)-1,2,3,4-Tetrahydronapthalen-1-ylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide | ||||||
Components | Carbonic anhydrase 12 | ||||||
Keywords | LYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor comple | ||||||
Function / homology | Function and homology information chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å | ||||||
Authors | Smirnov, A. / Manakova, E. / Grazulis, S. | ||||||
Citation | Journal: PeerJ / Year: 2018 Title: Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding. Authors: Smirnov, A. / Zubriene, A. / Manakova, E. / Grazulis, S. / Matulis, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5llp.cif.gz | 254 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5llp.ent.gz | 203.7 KB | Display | PDB format |
PDBx/mmJSON format | 5llp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5llp_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 5llp_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 5llp_validation.xml.gz | 55.7 KB | Display | |
Data in CIF | 5llp_validation.cif.gz | 81.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/5llp ftp://data.pdbj.org/pub/pdb/validation_reports/ll/5llp | HTTPS FTP |
-Related structure data
Related structure data | 5llcC 5lleC 5llgC 5llhC 5lloC 5msbC 1jd0S C: citing same article (ref.) S: Starting model for refinement |
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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: 29917.318 Da / Num. of mol.: 4 / Fragment: human carbonic anhydrase XII Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): rosetta / References: UniProt: O43570, carbonic anhydrase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-6Z9 / #4: 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: 2.08 Å3/Da / Density % sol: 40.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Crystallization buffer: 0.1M ammonium citrate (pH 7), 0.2M ammonium sulfate and 26% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.826606 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 23, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.826606 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.48→73.28 Å / Num. obs: 160218 / % possible obs: 98.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.282 Å2 / Rsym value: 0.062 / Net I/av σ(I): 5.961 / Net I/σ(I): 15.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JD0 Resolution: 1.48→73.28 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.0779 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.081 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.77 Å2 / Biso mean: 15.619 Å2 / Biso min: 3.16 Å2
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Refinement step | Cycle: final / Resolution: 1.48→73.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.518 Å / Total num. of bins used: 20
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