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- PDB-2jbk: membrane-bound glutamate carboxypeptidase II (GCPII) in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jbk | |||||||||
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Title | membrane-bound glutamate carboxypeptidase II (GCPII) in complex with quisqualic acid (quisqualate, alpha-amino-3,5-dioxo-1,2,4- oxadiazolidine-2-propanoic acid) | |||||||||
![]() | GLUTAMATE CARBOXYPEPTIDASE 2 | |||||||||
![]() | HYDROLASE / MULTIFUNCTIONAL ENZYME / NEURODEGENERATIVE DISEASE / GLYCOPROTEIN / METAL-BINDING / SIGNAL-ANCHOR / NAALADASE / DIPEPTIDASE / POLYMORPHISM / ZINC / PSMA / ANTIGEN / MEMBRANE / PROTEASE / PEPTIDASE / TRANSMEMBRANE / METAL- BINDING / METALLOPROTEASE / PROSTATE CANCER / CARBOXYPEPTIDASE | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mesters, J.R. / Henning, K. / Hilgenfeld, R. | |||||||||
![]() | ![]() Title: Human Glutamate Carboxypeptidase II Inhibition: Structures of Gcpii in Complex with Two Potent Inhibitors, Quisqualate and 2-Pmpa. Authors: Mesters, J.R. / Henning, K. / Hilgenfeld, R. #1: ![]() Title: Structure of Glutamate Carboxypeptidase II, a Drug Target in Neuronal Damage and Prostate Cancer Authors: Mesters, J.R. / Barinka, C. / Li, W. / Tsukamoto, T. / Majer, P. / Slusher, B.S. / Konvalinka, J. / Hilgenfeld, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.8 KB | Display | ![]() |
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PDB format | ![]() | 103.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2jbjC ![]() 2c6cS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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 / Fragment: EXTRACELLULAR PART, RESIDUES 44-750 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 7 molecules ![](data/chem/img/NAG.gif)
#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 #7: Sugar | |
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-Non-polymers , 5 types, 26 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/QUS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/QUS.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-QUS / ( | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | AMINO ACIDS 44-750 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.42 % / Description: NONE |
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Crystal grow | pH: 7 Details: 20 MM HEPES PH 7.25, 200 MM NACL, 5% (W/V) PEG 400 AND 15% (W/V) PEG 1500. |
-Data collection
Diffraction | Mean temperature: 260 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 27, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8115 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→50 Å / Num. obs: 20662 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.15 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2C6C Resolution: 2.99→100 Å / Cor.coef. Fo:Fc: 0.912 / SU B: 11.469 / SU ML: 0.211 / Cross valid method: THROUGHOUT / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.99→100 Å
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Refine LS restraints |
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