+Open data
-Basic information
Entry | Database: PDB / ID: 5nxo | |||||||||||||||
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Title | Carbonic Anhydrase II Inhibitor RA6 | |||||||||||||||
Components | Carbonic anhydrase 2 | |||||||||||||||
Keywords | LYASE / Carbonic Anhydrase II / CA Inhibitor | |||||||||||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å | |||||||||||||||
Authors | Brynda, J. / Rezacova, P. / Horejsi, M. / Fanfrlik, J. | |||||||||||||||
Funding support | Czech Republic, 4items
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Citation | Journal: Chemphyschem / Year: 2018 Title: Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes. Authors: Pecina, A. / Brynda, J. / Vrzal, L. / Gnanasekaran, R. / Horejsi, M. / Eyrilmez, S.M. / Rezac, J. / Lepsik, M. / Rezacova, P. / Hobza, P. / Majer, P. / Veverka, V. / Fanfrlik, J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nxo.cif.gz | 135.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nxo.ent.gz | 104.3 KB | Display | PDB format |
PDBx/mmJSON format | 5nxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nxo_validation.pdf.gz | 940 KB | Display | wwPDB validaton report |
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Full document | 5nxo_full_validation.pdf.gz | 939.6 KB | Display | |
Data in XML | 5nxo_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 5nxo_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/5nxo ftp://data.pdbj.org/pub/pdb/validation_reports/nx/5nxo | HTTPS FTP |
-Related structure data
Related structure data | 5nxgC 5nxiC 5nxmC 5nxpC 5nxvC 5nxwC 5ny1C 5ny3C 5ny6C 5nyaC 3po6S 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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Unit cell |
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-Components
#1: Protein | Mass: 29070.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 50 mM Tris 1.6 M Natrium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→41.05 Å / Num. obs: 70295 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 3.981 % / Biso Wilson estimate: 14.669 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.073 / Χ2: 1.023 / Net I/σ(I): 13.02 / Num. measured all: 279817 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3PO6 Resolution: 1.2→41.05 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.1404 / WRfactor Rwork: 0.1205 / FOM work R set: 0.8894 / SU B: 1.348 / SU ML: 0.027 / SU R Cruickshank DPI: 0.036 / SU Rfree: 0.0354 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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 / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.71 Å2 / Biso mean: 14.15 Å2 / Biso min: 6.47 Å2
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Refinement step | Cycle: final / Resolution: 1.2→41.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.198→1.229 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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