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Yorodumi- PDB-2wd2: A chimeric microtubule disruptor with efficacy on a taxane resist... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wd2 | ||||||
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Title | A chimeric microtubule disruptor with efficacy on a taxane resistant cell line | ||||||
Components | CARBONIC ANHYDRASE 2 | ||||||
Keywords | LYASE / DISEASE MUTATION / CANCER / HUMAN CARBONIC ANHYDRASE INHIBITORS / METAL-BINDING | ||||||
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 / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / 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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Leese, M.P. / Jourdan, F.L. / Kimberley, M.R. / Cozier, G.E. / Regis-Lydi, S. / Foster, P.A. / Newman, S.P. / Thiyagarajan, N. / Acharya, K.R. / Ferrandis, E. ...Leese, M.P. / Jourdan, F.L. / Kimberley, M.R. / Cozier, G.E. / Regis-Lydi, S. / Foster, P.A. / Newman, S.P. / Thiyagarajan, N. / Acharya, K.R. / Ferrandis, E. / Purohit, A. / Reed, M.J. / Potter, B.V.L. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2010 Title: Chimeric Microtubule Disruptors. Authors: Leese, M.P. / Jourdan, F.L. / Kimberley, M.R. / Cozier, G.E. / Thiyagarajan, N. / Stengel, C. / Regis-Lydi, S. / Foster, P.A. / Newman, S.P. / Acharya, K.R. / Ferrandis, E. / Purohit, A. / ...Authors: Leese, M.P. / Jourdan, F.L. / Kimberley, M.R. / Cozier, G.E. / Thiyagarajan, N. / Stengel, C. / Regis-Lydi, S. / Foster, P.A. / Newman, S.P. / Acharya, K.R. / Ferrandis, E. / Purohit, A. / Reed, M.J. / Potter, B.V.L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wd2.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wd2.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wd2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wd2_validation.pdf.gz | 726.9 KB | Display | wwPDB validaton report |
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Full document | 2wd2_full_validation.pdf.gz | 728.8 KB | Display | |
Data in XML | 2wd2_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 2wd2_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/2wd2 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/2wd2 | HTTPS FTP |
-Related structure data
Related structure data | 1ttmS 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: 29157.863 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-260 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MS5 / | #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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 MM TRIS-HCL, 1 MM ZNSO4, 2.5 M AMMONIUM SULFATE; 30 MM 2-MERCAPTOETHANOL, 0.5 MM 2-(3-METHOXYBENZYL)-6-O-SULFAMOYL-7-METHOXY-1,2,3,4- TETRAHYDROISOQUINOLINE, PH 8.0, VAPOUR DIFFUSION, ...Details: 100 MM TRIS-HCL, 1 MM ZNSO4, 2.5 M AMMONIUM SULFATE; 30 MM 2-MERCAPTOETHANOL, 0.5 MM 2-(3-METHOXYBENZYL)-6-O-SULFAMOYL-7-METHOXY-1,2,3,4- TETRAHYDROISOQUINOLINE, PH 8.0, VAPOUR DIFFUSION, HANGING DROP, TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 13, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→50 Å / Num. obs: 37376 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.49→1.54 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 62.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TTM Resolution: 1.49→25.93 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.53 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS ARE NOT MODELLED. THIS INCLUDES RESIDUES FROM 73-SQDK-76
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→25.93 Å
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Refine LS restraints |
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