+Open data
-Basic information
Entry | Database: PDB / ID: 6rzx | ||||||
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Title | Carbonic Anhydrase CAIX mimic in complex with inhibitor FBSA | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / carbonic anhydrase / 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 / regulation of intracellular pH / morphogenesis of an epithelium / 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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1 Å | ||||||
Authors | Kugler, M. / Brynda, J. / Rezacova, P. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: SLAS Discov / Year: 2020 Title: Identification of Novel Carbonic Anhydrase IX Inhibitors Using High-Throughput Screening of Pooled Compound Libraries by DNA-Linked Inhibitor Antibody Assay (DIANA). Authors: Tykvart, J. / Navratil, V. / Kugler, M. / Sacha, P. / Schimer, J. / Hlavackova, A. / Tenora, L. / Zemanova, J. / Dejmek, M. / Kral, V. / Potacek, M. / Majer, P. / Jahn, U. / Brynda, J. / ...Authors: Tykvart, J. / Navratil, V. / Kugler, M. / Sacha, P. / Schimer, J. / Hlavackova, A. / Tenora, L. / Zemanova, J. / Dejmek, M. / Kral, V. / Potacek, M. / Majer, P. / Jahn, U. / Brynda, J. / Rezacova, P. / Konvalinka, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rzx.cif.gz | 134.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rzx.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 6rzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/6rzx ftp://data.pdbj.org/pub/pdb/validation_reports/rz/6rzx | HTTPS FTP |
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-Related structure data
Related structure data | 6s03C 5ogpS 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: 29186.859 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 | ChemComp-KPQ / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris-H2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 10, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1→35.05 Å / Num. obs: 113106 / % possible obs: 87.5 % / Redundancy: 3.753 % / Biso Wilson estimate: 13.228 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.056 / Χ2: 1.06 / Net I/σ(I): 12.06 / Num. measured all: 424526 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5OGP Resolution: 1→35.05 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.84 / SU ML: 0.018 / SU R Cruickshank DPI: 0.0225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.024 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.89 Å2 / Biso mean: 15.319 Å2 / Biso min: 6.84 Å2
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Refinement step | Cycle: final / Resolution: 1→35.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.999→1.025 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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