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Open data
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Basic information
Entry | Database: PDB / ID: 9fxf | ||||||
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Title | VHH variant adression natural cytotoxicity triggering receptor 3 | ||||||
![]() | VHH | ||||||
![]() | IMMUNE SYSTEM / Natural killer cells / NKp30 / VHHs / humanization / molecular dynamics / Hallmark / framework residues / antigen recognition. | ||||||
Function / homology | 12-HYDROXYDODECANOIC ACID / PHOSPHATE ION![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Musil, D. / Freire, F. | ||||||
Funding support | 1items
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![]() | ![]() Title: On the humanization of VHHs: Prospective case studies, experimental and computational characterization of structural determinants for functionality. Authors: Fernandez-Quintero, M.L. / Guarnera, E. / Musil, D. / Pekar, L. / Sellmann, C. / Freire, F. / Sousa, R.L. / Santos, S.P. / Freitas, M.C. / Bandeiras, T.M. / Silva, M.M.S. / Loeffler, J.R. / ...Authors: Fernandez-Quintero, M.L. / Guarnera, E. / Musil, D. / Pekar, L. / Sellmann, C. / Freire, F. / Sousa, R.L. / Santos, S.P. / Freitas, M.C. / Bandeiras, T.M. / Silva, M.M.S. / Loeffler, J.R. / Ward, A.B. / Harwardt, J. / Zielonka, S. / Evers, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64 KB | Display | ![]() |
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PDB format | ![]() | 44.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.1 KB | Display | ![]() |
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Full document | ![]() | 432.3 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9fwwC 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
#1: Antibody | Mass: 14212.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-12H / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.5 M Ammonium phosphate, 0.1 M Sodium citrate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.067→24.522 Å / Num. obs: 37662 / % possible obs: 75.9 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.067→1.17 Å / Num. unique obs: 1883 / CC1/2: 0.828 / Rpim(I) all: 0.305 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 12.52 Å2
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Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.067→24.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.07→1.13 Å / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: -21.657 Å / Origin y: 5.1258 Å / Origin z: 13.539 Å
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Refinement TLS group | Selection details: { A|* } |