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Yorodumi- PDB-6skh: X-ray structure of human glutamate carboxypeptidase II (GCPII) - ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6skh | ||||||
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Title | X-ray structure of human glutamate carboxypeptidase II (GCPII) - the E424M inactive mutant, in complex with a inhibitor sulfamide inhibitor GluAsp | ||||||
Components | Glutamate carboxypeptidase 2 | ||||||
Keywords | HYDROLASE / glutamate carboxypeptidase II (GCPII) / NAALADase / prostate-specific membrane antigen / sulfamide | ||||||
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. / Novakova, Z. / Barinka, C. | ||||||
Citation | Journal: J.Chem.Inf.Model. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6skh.cif.gz | 192 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6skh.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 6skh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6skh_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 6skh_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 6skh_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 6skh_validation.cif.gz | 53.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/6skh ftp://data.pdbj.org/pub/pdb/validation_reports/sk/6skh | HTTPS FTP |
-Related structure data
Related structure data | 4w9yC 6sgpC 3bi1S S: Starting model for refinement C: citing same article (ref.) |
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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: 79616.828 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 / Production host: Drosophila melanogaster (fruit fly) / Variant (production host): Schneiders S2 cells / References: UniProt: Q04609, glutamate carboxypeptidase II |
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-Sugars , 6 types, 8 molecules
#2: 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 | ||||||||
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#3: Polysaccharide | 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: 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 #6: Sugar | #11: Sugar | ChemComp-BMA / | |
-Non-polymers , 8 types, 602 molecules
#7: Chemical | ChemComp-EDO / #8: Chemical | #9: Chemical | ChemComp-CA / | #10: Chemical | ChemComp-CL / | #12: Chemical | ChemComp-PEG / | #13: Chemical | ChemComp-LHK / ( | #14: Chemical | ChemComp-GOL / | #15: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.36 Å3/Da / Density % sol: 63.44 % |
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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, 2 % (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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 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: 143110 / % possible obs: 99.2 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.042 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 29834 / CC1/2: 0.86 / Rrim(I) all: 0.678 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3BI1 Resolution: 1.58→49.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.071 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: 128.96 Å2 / Biso mean: 29.211 Å2 / Biso min: 14.54 Å2
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Refinement step | Cycle: final / Resolution: 1.58→49.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.62 Å
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