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- PDB-7coz: Crystal Structure of double mutant Y115E Y117E human Secretory Gl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7coz | ||||||
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Title | Crystal Structure of double mutant Y115E Y117E human Secretory Glutaminyl Cyclase in complex with LSB-41 | ||||||
![]() | Glutaminyl-peptide cyclotransferase![]() | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dileep, K.V. / Ihara, K. / Sakai, N. / Shirozu, M. / Zhang, K.Y.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Piperidine-4-carboxamide as a new scaffold for designing secretory glutaminyl cyclase inhibitors. Authors: Dileep, K.V. / Sakai, N. / Ihara, K. / Kato-Murayama, M. / Nakata, A. / Ito, A. / Sivaraman, D.M. / Shin, J.W. / Yoshida, M. / Shirouzu, M. / Zhang, K.Y.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 | ![]() | 225.4 KB | Display | ![]() |
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PDB format | ![]() | 178.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cp0C ![]() 4ywyS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | ![]() Mass: 37331.121 Da / Num. of mol.: 3 / Mutation: Y115E, Y117E Source method: isolated from a genetically manipulated source Details: Cpd-41 / Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: Q16769, ![]() |
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-Non-polymers , 5 types, 806 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/Q39.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/Q39.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ![]() #4: Chemical | #5: Chemical | ChemComp-EDO / ![]() #6: 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: 2.72 Å3/Da / Density % sol: 54.85 % / Description: Hexagonal plate like crystals |
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Crystal grow![]() | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 100 mM MES buffer pH 6.0-6.5, 46-67 mM NaOH, 100 mM ammonium sulfate PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 15, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||
Reflection | Resolution: 1.85→43.03 Å / Num. obs: 101712 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.147 / Net I/σ(I): 9.6 / Num. measured all: 773340 / Scaling rejects: 42 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4YWY Resolution: 1.85→43.03 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 94.17 Å2 / Biso mean: 20.7969 Å2 / Biso min: 5.53 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→43.03 Å
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LS refinement shell | Resolution: 1.85→1.87 Å
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