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- PDB-8t8i: Structure of VHH-Fab complex with engineered Elbow FNQIKG, Crysta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8t8i | ||||||
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Title | Structure of VHH-Fab complex with engineered Elbow FNQIKG, Crystal Kappa and SER substitutions | ||||||
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![]() | IMMUNE SYSTEM / NabFab / Nanobody / Antibody Fragment | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / SUCCINIC ACID![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Filippova, E.V. / Thompson, I. / Kossiakoff, A.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes. Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / ...Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / Atwell, S. / Kossiakoff, A.A. / Sidhu, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.1 KB | Display | ![]() |
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PDB format | ![]() | 190.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t58C ![]() 8t6iC ![]() 8t7fC ![]() 8t7gC ![]() 8t7iC ![]() 8t9yC ![]() 8trsC ![]() 8trtC ![]() 8ts5C 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
-Antibody , 3 types, 3 molecules ALH
#1: Antibody | Mass: 14170.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 23018.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: "QGTTS" - Crystal Kappa substitution "Q149S" and "K150Y" - SER substitution Source: (gene. exp.) ![]() ![]() ![]() |
#3: Antibody | Mass: 25753.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: "FNQIKG" - elbow region substitution / Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 76 molecules ![](data/chem/img/SIN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SIN / | ||||
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#5: Chemical | ChemComp-PEG / | ||||
#6: Chemical | #7: Chemical | #8: 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: 3.72 Å3/Da / Density % sol: 66.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2% Tacsimate pH 5.0, 0.1 M Na citrate tribasic dihydrate, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→121.2 Å / Num. obs: 32276 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.99 / Rpim(I) all: 0.04 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.52→2.62 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3603 / CC1/2: 0.37 / Rpim(I) all: 0.78 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.249 Å2
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Refinement step | Cycle: 1 / Resolution: 2.52→121.2 Å
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Refine LS restraints |
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