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Open data
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Basic information
Entry | Database: PDB / ID: 6rqm | ||||||
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Title | A blocking anti-CTLA-4 Nanobody (KN044) complexed with CTLA-4 | ||||||
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![]() | IMMUNE SYSTEM / Antibody / check-point / CTLA-4 / receptor | ||||||
Function / homology | ![]() protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response ...protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response / immune response / positive regulation of apoptotic process / external side of plasma membrane / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, F. / Zhou, A. / Gao, H. | ||||||
![]() | ![]() Title: A blocking anti-CTLA-4 Nanobody (KN044) complexed with CTLA-4 Authors: Gao, H. / Zhou, 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 | ![]() | 103.3 KB | Display | ![]() |
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PDB format | ![]() | 80.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.1 KB | Display | ![]() |
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Full document | ![]() | 426.3 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Antibody | Mass: 15308.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal His-tag residues are missing due to weak electron density. Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 13381.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: missing residues due to weak electron density / Source: (gene. exp.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 3→68 Å / Num. obs: 6820 / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.032 / Rrim(I) all: 0.121 / Χ2: 1.03 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 3 / Num. unique obs: 1068 / Χ2: 0.99 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JDS, 3OSK Resolution: 3→67.73 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.887 / SU B: 62.596 / SU ML: 0.469 / Cross valid method: THROUGHOUT / ESU R Free: 0.501 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.615 Å2
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Refinement step | Cycle: LAST / Resolution: 3→67.73 Å
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Refine LS restraints |
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