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Yorodumi- PDB-4zwz: Engineered Carbonic Anhydrase IX mimic in complex with a glucosyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zwz | ||||||
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Title | Engineered Carbonic Anhydrase IX mimic in complex with a glucosyl sulfamate inhibitor | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / Carbonic Anhydrase IX mimic / glucosyl sulfamate / inhibitor complex. / LYASE-LYASE INHIBITOR complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Mahon, B.P. / Lomelino, C.L. / Driscoll, J.M. / McKenna, R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Mapping Selective Inhibition of the Cancer-Related Carbonic Anhydrase IX Using Structure-Activity Relationships of Glucosyl-Based Sulfamates. Authors: Mahon, B.P. / Lomelino, C.L. / Ladwig, J. / Rankin, G.M. / Driscoll, J.M. / Salguero, A.L. / Pinard, M.A. / Vullo, D. / Supuran, C.T. / Poulsen, S.A. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zwz.cif.gz | 130.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zwz.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zwz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zwz_validation.pdf.gz | 811.7 KB | Display | wwPDB validaton report |
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Full document | 4zwz_full_validation.pdf.gz | 814.7 KB | Display | |
Data in XML | 4zwz_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 4zwz_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/4zwz ftp://data.pdbj.org/pub/pdb/validation_reports/zw/4zwz | HTTPS FTP |
-Related structure data
Related structure data | 4zwxC 4zwyC 4zx0C 4zx1C 3ks3S 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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Unit cell |
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-Components
#1: Protein | Mass: 28844.465 Da / Num. of mol.: 1 / Fragment: UNP residues 4-260 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A 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: Sugar | ChemComp-510 / | ||
#4: Chemical | #5: 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: 2.06 Å3/Da / Density % sol: 40.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris-HCl pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 17, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.62→20 Å / Num. obs: 27416 / % possible obs: 90.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.83 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.025 / Rrim(I) all: 0.05 / Χ2: 0.785 / Net I/av σ(I): 24.343 / Net I/σ(I): 13 / Num. measured all: 96724 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 1.62→19.749 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.35 Å2 / Biso mean: 21.6383 Å2 / Biso min: 8.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.62→19.749 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: 11.8569 Å / Origin y: -1.4328 Å / Origin z: 15.8297 Å
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Refinement TLS group |
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