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Open data
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Basic information
Entry | Database: PDB / ID: 7d4b | ||||||
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Title | Crystal structure of 4-1BB in complex with a VHH | ||||||
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![]() | IMMUNE SYSTEM / antibody / Complex / VHH | ||||||
Function / homology | ![]() TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / signaling receptor activity / regulation of cell population proliferation / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, C. | ||||||
![]() | ![]() Title: Generation of a safe and efficacious llama single-domain antibody fragment (vHH) targeting the membrane-proximal region of 4-1BB for engineering therapeutic bispecific antibodies for cancer. Authors: Zhai, T. / Wang, C. / Xu, Y. / Huang, W. / Yuan, Z. / Wang, T. / Dai, S. / Peng, S. / Pang, T. / Jiang, W. / Huang, Y. / Zou, Y. / Xu, Y. / Sun, J. / Gong, X. / Zhang, J. / Tsun, A. / Li, B. / Miao, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.1 KB | Display | ![]() |
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PDB format | ![]() | 52 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7czdC ![]() 4xtaS ![]() 6mgpS 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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Unit cell |
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Components
-Protein / Antibody , 2 types, 2 molecules AB
#1: Protein | Mass: 15046.007 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 13852.370 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 2 types, 2 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 15 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8.5 Details: 1.5 M lithium sulfate, 100 mM Tris (pH 8.5), 10 mM nickel sulfate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.14→47.79 Å / Num. obs: 15429 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.047 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 3.14→3.36 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.241 / Num. unique obs: 2723 / CC1/2: 0.894 / Rpim(I) all: 0.359 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6MGP, 4XTA Resolution: 3.14→47.79 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.918 / SU B: 15.886 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.409 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 258.79 Å2 / Biso mean: 90.054 Å2 / Biso min: 46.83 Å2
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Refinement step | Cycle: final / Resolution: 3.14→47.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.14→3.222 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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