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- PDB-8xgt: Crystal structure of human secretory glutaminyl cyclase in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8xgt | ||||||
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Title | Crystal structure of human secretory glutaminyl cyclase in complex with (Z)-3-((1H-benzo[d]imidazol-5-yl)methylene)-4-hydroxyindolin-2-one | ||||||
![]() | Glutaminyl-peptide cyclotransferase | ||||||
![]() | TRANSFERASE / inhibitor / complex | ||||||
Function / homology | ![]() peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / protein modification process / specific granule lumen / tertiary granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, G.-B. / Wang, X.-Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray Structure-Guided Discovery of a Potent Benzimidazole Glutaminyl Cyclase Inhibitor That Shows Activity in a Parkinson's Disease Mouse Model. Authors: Mou, J. / Ning, X.L. / Wang, X.Y. / Hou, S.Y. / Meng, F.B. / Zhou, C. / Wu, J.W. / Li, C. / Jia, T. / Wu, X. / Wu, Y. / Chen, Y. / Li, G.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 776.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8xfvC ![]() 8xgaC ![]() 8xgbC ![]() 8xgyC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37557.398 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q16769, glutaminyl-peptide cyclotransferase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-A1D48 / ( Mass: 277.277 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H11N3O2 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 12% -16% PEG 4000, 0.2M MgCl2, 0.1M Tris HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→161.83 Å / Num. obs: 107900 / % possible obs: 99.3 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.051 / Rrim(I) all: 0.125 / Χ2: 0.98 / Net I/σ(I): 13.5 / Num. measured all: 646754 |
Reflection shell | Resolution: 2.81→2.96 Å / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.883 / Num. measured all: 94452 / Num. unique obs: 15619 / CC1/2: 0.815 / Rpim(I) all: 0.391 / Rrim(I) all: 0.967 / Χ2: 0.88 / Net I/σ(I) obs: 2.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.813→54.857 Å
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Refine LS restraints |
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LS refinement shell |
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