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Yorodumi- PDB-5of0: X-ray structure of human glutamate carboxypeptidase II (GCPII), t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5of0 | |||||||||
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Title | X-ray structure of human glutamate carboxypeptidase II (GCPII), the E424M inactive mutant, in complex with a inhibitor CFBzOG | |||||||||
Components | Glutamate carboxypeptidase 2 | |||||||||
Keywords | HYDROLASE / glutamate carboxypeptidase II (GCPII) / NAALADase / prostate-specific membrane antigen / urea based inhibitor | |||||||||
Function / homology | Function and homology information C-terminal protein deglutamylation / Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / Aspartate and asparagine metabolism / dipeptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / peptidase activity ...C-terminal protein deglutamylation / Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / 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 / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | |||||||||
Authors | Novakova, Z. / Motlova, L. / Barinka, C. | |||||||||
Citation | Journal: ACS Med Chem Lett / Year: 2018 Title: 2-Aminoadipic Acid-C(O)-Glutamate Based Prostate-Specific Membrane Antigen Ligands for Potential Use as Theranostics. Authors: Nakajima, R. / Novakova, Z. / Tueckmantel, W. / Motlova, L. / Barinka, C. / Kozikowski, A.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5of0.cif.gz | 337.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5of0.ent.gz | 271.4 KB | Display | PDB format |
PDBx/mmJSON format | 5of0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/5of0 ftp://data.pdbj.org/pub/pdb/validation_reports/of/5of0 | HTTPS FTP |
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-Related structure data
Related structure data | 6h7yC 6h7zC 6hkjC 6hkzC 3bi1S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 79616.828 Da / Num. of mol.: 1 / Mutation: E424M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27 / Cell line (production host): Schneiders S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q04609, glutamate carboxypeptidase II |
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-Sugars , 4 types, 7 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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 #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 #5: Sugar | |
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-Non-polymers , 5 types, 619 molecules
#6: Chemical | #7: Chemical | ChemComp-CA / | #8: Chemical | ChemComp-CL / | #9: Chemical | ChemComp-9TB / ( | #10: 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: 3.32 Å3/Da / Density % sol: 62.91 % |
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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, 2 % (w/v) PEG 3350, and 100 mM Tris-HCl, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2017 |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→49.25 Å / Num. obs: 173724 / % possible obs: 98.9 % / Redundancy: 5.2 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.018 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.48→1.5 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8104 / CC1/2: 0.849 / Rpim(I) all: 0.314 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BI1 Resolution: 1.48→49.25 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.304 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.483 Å2
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Refinement step | Cycle: 1 / Resolution: 1.48→49.25 Å
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Refine LS restraints |
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