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- PDB-8xga: Crystal structure of human Golgi resident glutaminyl cyclase in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8xga | ||||||
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Title | Crystal structure of human Golgi resident glutaminyl cyclase in complex with (Z)-3-((1H-benzo[d]imidazol-5-yl)methylene)-4-((tetrahydro-2H-pyran-4-yl)oxy)indolin-2-one | ||||||
![]() | Glutaminyl-peptide cyclotransferase-like protein | ||||||
![]() | TRANSFERASE / inhibitor / complex | ||||||
Function / homology | ![]() peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / Golgi membrane / Golgi apparatus / zinc ion binding / membrane 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 | ![]() | 672.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 128.8 KB | Display | |
Data in CIF | ![]() | 167.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8xfvC ![]() 8xgbC ![]() 8xgtC ![]() 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: 34989.387 Da / Num. of mol.: 11 Source method: isolated from a genetically manipulated source Details: Homo sapiens / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NXS2, glutaminyl-peptide cyclotransferase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-A1D47 / ( Mass: 361.394 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C21H19N3O3 / 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: 2.73 Å3/Da / Density % sol: 54.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25%-28% PEG 3350, 0.1M HEPES, pH 7.5 |
-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: 3.537→154.66 Å / Num. obs: 48967 / % possible obs: 96.3 % / Redundancy: 3.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.085 / Rrim(I) all: 0.16 / Χ2: 0.44 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 3.54→3.73 Å / % possible obs: 85.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.468 / Num. measured all: 20869 / Num. unique obs: 6301 / CC1/2: 0.83 / Rpim(I) all: 0.299 / Rrim(I) all: 0.557 / Χ2: 0.43 / Net I/σ(I) obs: 2.1 |
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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: 3.537→74.279 Å
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Refine LS restraints |
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LS refinement shell |
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