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Yorodumi- PDB-4oc2: X-ray structure of of human glutamate carboxypeptidase II (GCPII)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oc2 | |||||||||
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Title | X-ray structure of of human glutamate carboxypeptidase II (GCPII) in a complex with CEIBzL, a urea-based inhibitor N~2~-{[(1S)-1-carboxybut-3-yn-1-yl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine | |||||||||
Components | Glutamate carboxypeptidase 2 | |||||||||
Keywords | hydrolase/hydrolase inhibitor / hydrolase / metallopeptidase / hydrolase-hydrolase inhibitor complex | |||||||||
Function / homology | Function and homology information Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / C-terminal protein deglutamylation / Aspartate and asparagine metabolism / dipeptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / peptidase activity ...Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / C-terminal protein deglutamylation / Aspartate and asparagine metabolism / dipeptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / peptidase activity / cell surface / proteolysis / extracellular exosome / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å | |||||||||
Authors | Pavlicek, J. / Ptacek, J. / Cerny, J. / Byun, Y. / Skultetyova, L. / Pomper, M. / Lubkowski, J. / Barinka, C. | |||||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2014 Title: Structural characterization of P1'-diversified urea-based inhibitors of glutamate carboxypeptidase II. Authors: Pavlicek, J. / Ptacek, J. / Cerny, J. / Byun, Y. / Skultetyova, L. / Pomper, M.G. / Lubkowski, J. / Barinka, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oc2.cif.gz | 331.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oc2.ent.gz | 272.3 KB | Display | PDB format |
PDBx/mmJSON format | 4oc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oc2_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 4oc2_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 4oc2_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 4oc2_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/4oc2 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/4oc2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 79859.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider's S2 cells / References: UniProt: Q04609, glutamate carboxypeptidase II |
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-Sugars , 6 types, 7 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#7: Sugar |
-Non-polymers , 5 types, 539 molecules
#8: Chemical | #9: Chemical | ChemComp-CA / | #10: Chemical | ChemComp-CL / | #11: Chemical | ChemComp-2QQ / | #12: 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: 3.29 Å3/Da / Density % sol: 62.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 33% (v/v) pentaerythritol propoxylate PO/OH 5/4, 1% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 24, 2009 |
Radiation | Monochromator: Si 220. Rosenbaum-Rock double-crystal monochromator. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 124655 / Num. obs: 124655 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.65→1.71 Å / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.65→29.47 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.18 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.073 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.025 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→29.47 Å
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Refine LS restraints |
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