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Yorodumi- PDB-5o5r: X-ray structure of human glutamate carboxypeptidase II (GCPII) in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o5r | |||||||||
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Title | X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a urea based inhibitor PSMA 1023 | |||||||||
Components | Glutamate carboxypeptidase 2 | |||||||||
Keywords | HYDROLASE / glutamate carboxypeptidase II (GCPII) / NAALADase / prostate-specific membrane antigen / urea based inhibitor | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Motlova, L. / Novakova, Z. / Barinka, C. | |||||||||
Citation | Journal: To Be Published Title: X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a urea based inhibitor PSMA 1023 Authors: Motlova, L. / Novakova, Z. / Barinka, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o5r.cif.gz | 363.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o5r.ent.gz | 293.2 KB | Display | PDB format |
PDBx/mmJSON format | 5o5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o5r_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 5o5r_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 5o5r_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 5o5r_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/5o5r ftp://data.pdbj.org/pub/pdb/validation_reports/o5/5o5r | HTTPS FTP |
-Related structure data
Related structure data | 3bi1S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 79614.750 Da / Num. of mol.: 1 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 , 5 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 | 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 |
#4: 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 |
#5: 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 |
#7: Sugar |
-Non-polymers , 7 types, 632 molecules
#6: Chemical | ChemComp-9OQ / ( | ||||||||||
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#8: Chemical | #9: Chemical | ChemComp-CA / | #10: Chemical | ChemComp-CL / | #11: Chemical | #12: Chemical | ChemComp-EDO / | #13: 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: 3.3 Å3/Da / Density % sol: 62.76 % / Description: clear block, 50 x 200 um |
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Crystal grow | Temperature: 293.15 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: 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: 1.65→49.13 Å / Num. obs: 125247 / % possible obs: 99.1 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.029 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5979 / CC1/2: 0.762 / Rpim(I) all: 0.493 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BI1.pdb Resolution: 1.65→49.13 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 3.181 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.065 / 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: 36.995 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→49.13 Å
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Refine LS restraints |
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