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Yorodumi- PDB-6h7z: X-ray structure of human glutamate carboxypeptidase II (GCPII) in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h7z | |||||||||
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Title | X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor RNA 2-65-1 | |||||||||
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 / FOURIER SYNTHESIS / Resolution: 2 Å | |||||||||
Authors | Motlova, L. / Novakova, Z. / 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 | 6h7z.cif.gz | 346.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h7z.ent.gz | 279.5 KB | Display | PDB format |
PDBx/mmJSON format | 6h7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/6h7z ftp://data.pdbj.org/pub/pdb/validation_reports/h7/6h7z | HTTPS FTP |
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-Related structure data
Related structure data | 5of0C 6h7yC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 79614.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: D654 was in the experimant, but could not be fitted into map.. Source: (gene. exp.) Homo sapiens (human) / Gene: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27 / Production host: Drosophila melanogaster (fruit fly) / Variant (production host): Schneiders S2 cells / References: UniProt: Q04609, glutamate carboxypeptidase II |
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-Sugars , 4 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 #3: 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 #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 #8: Sugar | ChemComp-NAG / | |
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-Non-polymers , 8 types, 561 molecules
#5: Chemical | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-CL / | #9: Chemical | #10: Chemical | ChemComp-EDO / #11: Chemical | ChemComp-TRS / | #12: Chemical | ChemComp-FVW / ( | #13: 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: 3.28 Å3/Da / Density % sol: 62.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 34% (v/v) pentaerythritol propoxylate PO/OH 5/4, 2 % (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Dec 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34 Å / Relative weight: 1 |
Reflection | Resolution: 2→30.8 Å / Num. obs: 70883 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4537 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3BI1 Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.296 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.134 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.254 Å2
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Refinement step | Cycle: 1 / Resolution: 2→30 Å
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Refine LS restraints |
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