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Yorodumi- PDB-3d7f: A high resolution crystal structure of human glutamate carboxypep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d7f | |||||||||
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Title | A high resolution crystal structure of human glutamate carboxypeptidase II (GCPII) in a complex with DCIT, a urea-based inhibitor | |||||||||
Components | Glutamate carboxypeptidase 2 | |||||||||
Keywords | HYDROLASE / prostate specific membrane antigen / metallopeptidase / folate hydrolase / glutamate carboxypeptidase II / NAALADase / DCIT / urea-based inhibitor / Carboxypeptidase / Dipeptidase / Glycoprotein / Membrane / Metal-binding / Metalloprotease / Multifunctional enzyme / Protease / Signal-anchor / Transmembrane | |||||||||
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: 1.54 Å | |||||||||
Authors | Lubkowski, J. / Barinka, C. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Interactions between Human Glutamate Carboxypeptidase II and Urea-Based Inhibitors: Structural Characterization Authors: Barinka, C. / Byun, Y. / Dusich, C.L. / Banerjee, S.R. / Chen, Y. / Castanares, M. / Kozikowski, A.P. / Mease, R.C. / Pomper, M.G. / Lubkowski, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d7f.cif.gz | 182.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d7f.ent.gz | 140.3 KB | Display | PDB format |
PDBx/mmJSON format | 3d7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d7f_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 3d7f_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 3d7f_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 3d7f_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/3d7f ftp://data.pdbj.org/pub/pdb/validation_reports/d7/3d7f | HTTPS FTP |
-Related structure data
Related structure data | 3d7dC 3d7gC 3d7hC 2ootS C: citing same article (ref.) 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 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: FOLH1, FOLH, NAALAD1, PSM, PSMA / Cell line (production host): Schneider's 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 | 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)-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 #5: Sugar | |
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-Non-polymers , 5 types, 662 molecules
#6: Chemical | #7: Chemical | ChemComp-CA / | #8: Chemical | ChemComp-CL / | #9: Chemical | ChemComp-YBY / | #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: 3.27 Å3/Da / Density % sol: 62.43 % |
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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-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→30 Å / Num. all: 144557 / Num. obs: 144557 / % possible obs: 95 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.54→1.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.2 / Num. unique all: 9835 / % possible all: 65.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2oot Resolution: 1.54→15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.345 / SU ML: 0.047 / Isotropic thermal model: mixed isotropic/anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 27.494 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.544→1.584 Å / Total num. of bins used: 20
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