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Yorodumi- PDB-8bow: X-ray structure of human glutamate carboxypeptidase II (GCPII) in... -
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-Basic information
Entry | Database: PDB / ID: 8bow | ||||||
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Title | X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with an inhibitor 617 | ||||||
Components | Glutamate carboxypeptidase 2 | ||||||
Keywords | HYDROLASE / glutamate carboxypeptidase II (GCPII) / NAALADase / prostate-specific membrane antigen / 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 / FOURIER SYNTHESIS / Resolution: 1.58 Å | ||||||
Authors | Motlova, L. / Barinka, C. / Benesova, M. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with an inhibitor 617 Authors: Motlova, L. / Barinka, C. / Benesova, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bow.cif.gz | 188.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bow.ent.gz | 142.7 KB | Display | PDB format |
PDBx/mmJSON format | 8bow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bow_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8bow_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8bow_validation.xml.gz | 35 KB | Display | |
Data in CIF | 8bow_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/8bow ftp://data.pdbj.org/pub/pdb/validation_reports/bo/8bow | HTTPS FTP |
-Related structure data
Related structure data | 3bi1S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: The electron density map was not sufficient for missing residues due to their flexibility. Source: (gene. exp.) Homo sapiens (human) / Gene: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneiders S2 cells / References: UniProt: Q04609, glutamate carboxypeptidase II |
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-Sugars , 5 types, 7 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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 #4: 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 #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-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 #9: Sugar | |
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-Non-polymers , 5 types, 640 molecules
#6: Chemical | #7: Chemical | ChemComp-CA / | #8: Chemical | ChemComp-CL / | #10: Chemical | ChemComp-QYF / ( | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-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: 62.69 % |
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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 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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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: Aug 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. obs: 143725 / % possible obs: 99.5 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.061 / Net I/σ(I): 17.86 |
Reflection shell | Resolution: 1.58→1.67 Å / Redundancy: 4.98 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 22658 / CC1/2: 0.805 / Rrim(I) all: 0.793 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3BI1 Resolution: 1.58→45.25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.584 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.069 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.284 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→45.25 Å
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Refine LS restraints |
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