+
Open data
-
Basic information
Entry | Database: PDB / ID: 8utk | ||||||
---|---|---|---|---|---|---|---|
Title | IL-23R minibinder - 23R-B04dslf02IB | ||||||
![]() | 23R-B04dslf02IB | ||||||
![]() | DE NOVO PROTEIN / Computational design / selective inhibitors / IL-2 IL-17 cytokines DE NOVO PROTEIN | ||||||
Function / homology | 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Chem-PG6![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bera, A.K. / Berger, S.A. / Kang, A. / Baker, D. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Preclinical proof of principle for orally delivered Th17 antagonist miniproteins. Authors: Berger, S. / Seeger, F. / Yu, T.Y. / Aydin, M. / Yang, H. / Rosenblum, D. / Guenin-Mace, L. / Glassman, C. / Arguinchona, L. / Sniezek, C. / Blackstone, A. / Carter, L. / Ravichandran, R. / ...Authors: Berger, S. / Seeger, F. / Yu, T.Y. / Aydin, M. / Yang, H. / Rosenblum, D. / Guenin-Mace, L. / Glassman, C. / Arguinchona, L. / Sniezek, C. / Blackstone, A. / Carter, L. / Ravichandran, R. / Ahlrichs, M. / Murphy, M. / Pultz, I.S. / Kang, A. / Bera, A.K. / Stewart, L. / Garcia, K.C. / Naik, S. / Spangler, J.B. / Beigel, F. / Siebeck, M. / Gropp, R. / Baker, D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 42.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 23.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 763 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 763 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 6398.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Chemical | ChemComp-PG6 / | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-PG5 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.6 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2 M Lithium sulfate 0.1 M Sodium acetate pH 4.5 and 50% (v/v) PEG 400. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→47.99 Å / Num. obs: 11624 / % possible obs: 98.79 % / Redundancy: 20 % / Biso Wilson estimate: 38.93 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.511 / Rpim(I) all: 0.1164 / Net I/σ(I): 3.62 |
Reflection shell | Resolution: 1.94→2.009 Å / Redundancy: 20.4 % / Rmerge(I) obs: 2.587 / Mean I/σ(I) obs: 0.77 / Num. unique obs: 1121 / CC1/2: 0.372 / Rpim(I) all: 0.5828 / % possible all: 98.16 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.43 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→47.99 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|