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- PDB-8gk2: Porous framework formed by assembly of a bipyridyl-conjugated hel... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gk2 | ||||||
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Title | Porous framework formed by assembly of a bipyridyl-conjugated helical peptide | ||||||
![]() | LEU-AIB-ALA-SER-LEU-ALA-CYS-AIB-LEU | ||||||
![]() | DE NOVO PROTEIN | ||||||
Function / homology | SILVER ION / Chem-I77 / NICOTINIC ACID / NITRATE ION![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hess, S.S. / Nguyen, A.I. | ||||||
Funding support | 1items
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![]() | ![]() Title: Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks. Authors: Hess, S.S. / Coppola, F. / Dang, V.T. / Tran, P.N. / Mickel, P.J. / Oktawiec, J. / Ren, Z. / Kral, P. / Nguyen, A.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 21.3 KB | Display | ![]() |
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PDB format | ![]() | 11.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 849.8 KB | Display | ![]() |
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Full document | ![]() | 852.8 KB | Display | |
Data in XML | ![]() | 3.8 KB | Display | |
Data in CIF | ![]() | 4.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gb9C ![]() 8gbaC ![]() 8gbhC ![]() 8gbiC ![]() 8gbmC ![]() 8gboC ![]() 8gd6C ![]() 8gd8C ![]() 8givC ![]() 8gj7C ![]() 8gk1C ![]() 8gk9C ![]() 8gkbC ![]() 8gkxC ![]() 8gl0C ![]() 8gl4C ![]() 8gl5C ![]() 8sw2C ![]() 8sy4C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | Mass: 860.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 15 molecules ![](data/chem/img/NIO.gif)
![](data/chem/img/I77.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/AG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/I77.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/AG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NIO / | ||
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#3: Chemical | ChemComp-I77 / | ||
#4: Chemical | ChemComp-NO3 / | ||
#5: Chemical | ChemComp-AG / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.61 % |
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Crystal grow | Temperature: 298 K / Method: slow cooling / Details: Water/Acetontrile |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.61984 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→16.72 Å / Num. obs: 11349 / % possible obs: 98.04 % / Redundancy: 11.9 % / Biso Wilson estimate: 7.34 Å2 / Rmerge(I) obs: 0.1723 / Net I/σ(I): 9.29 |
Reflection shell | Resolution: 0.89→0.9218 Å / Rmerge(I) obs: 0.8058 / Num. unique obs: 574 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 7.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.89→16.72 Å
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Refine LS restraints |
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LS refinement shell |
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