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- PDB-6sgp: X-ray structure of human glutamate carboxypeptidase II (GCPII) - ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sgp | ||||||
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Title | X-ray structure of human glutamate carboxypeptidase II (GCPII) - the E424M inactive mutant, in complex with a sulfamide inhibitor GluGlu | ||||||
![]() | Glutamate carboxypeptidase 2 | ||||||
![]() | HYDROLASE / glutamate carboxypeptidase II (GCPII) / NAALADase / prostate-specific membrane antigen / sulfamide | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Barinka, C. / Shukla, S. / Motlova, L. | ||||||
![]() | ![]() Title: Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors. Authors: Novakova, Z. / Tehrani, Z.A. / Jurok, R. / Motlova, L. / Kutil, Z. / Pavlicek, J. / Shukla, S. / Choy, C.J. / Havlinova, B. / Baranova, P. / Berkman, C.E. / Kuchar, M. / Cerny, J. / Barinka, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.8 KB | Display | ![]() |
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PDB format | ![]() | 138.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 33.1 KB | Display | |
Data in CIF | ![]() | 49.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4w9yC ![]() 6skhC ![]() 3bi1S 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: 79616.828 Da / Num. of mol.: 1 / Mutation: E424M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 4 types, 7 molecules ![](data/chem/img/NAG.gif)
#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 | 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 #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 #5: Sugar | ChemComp-NAG / | |
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-Non-polymers , 8 types, 443 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/LDK.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/LDK.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-CA / | #8: Chemical | ChemComp-CL / | #9: Chemical | ChemComp-PGE / | #10: Chemical | #11: Chemical | ChemComp-LDK / ( | #12: Chemical | ChemComp-NA / | #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.37 % |
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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: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. obs: 141047 / % possible obs: 97 % / Redundancy: 4.4 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.045 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.58→1.67 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.689 / Num. unique obs: 22618 / CC1/2: 0.83 / Rrim(I) all: 0.789 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BI1 Resolution: 1.58→46.9 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.072 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 122.4 Å2 / Biso mean: 30.564 Å2 / Biso min: 16.38 Å2
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Refinement step | Cycle: final / Resolution: 1.58→46.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.619 Å
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