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- PDB-8hy3: 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: 8hy3 | ||||||
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Title | Crystal structure of human secretory glutaminyl cyclase in complex with 1-benzyl-5-methyl-1H-imidazole | ||||||
![]() | 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. / Deng, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of human secretory glutaminyl cyclase in complex with 1-benzyl-5-methyl-1H-imidazole Authors: Li, G.-B. / Deng, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.1 KB | Display | ![]() |
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PDB format | ![]() | 108.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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: 37557.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q16769, glutaminyl-peptide cyclotransferase |
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-Non-polymers , 5 types, 46 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-4Q8 / Mass: 172.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2 / Feature type: SUBJECT OF INVESTIGATION |
#4: Chemical | ChemComp-CO2 / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.7 Å3/Da / Density % sol: 78.43 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 14%-18% (v/v) PEG 4000, 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 198 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Dec 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→20.03 Å / Num. obs: 64779 / % possible obs: 99.79 % / Redundancy: 76.1 % / Rmerge(I) obs: 0.448 / Rpim(I) all: 0.051 / Rrim(I) all: 0.451 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.94→2.01 Å / Num. unique obs: 6251 / CC1/2: 0.009 |
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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: 1.952→19.618 Å
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Refine LS restraints |
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LS refinement shell |
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