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- PDB-6k0y: Study of the interactions of a novel monoclonal antibody, mAb059c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k0y | ||||||
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Title | Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor | ||||||
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![]() | IMMUNE SYSTEM / PD-1 Complex / Immune Checkpoint / Inhibitor | ||||||
Function / homology | ![]() negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response / PD-1 signaling / signaling receptor activity / adaptive immune response / Potential therapeutics for SARS / external side of plasma membrane / apoptotic process / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, J.X. / Wang, G.Q. | ||||||
![]() | ![]() Title: Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor. Authors: Liu, J. / Wang, G. / Liu, L. / Wu, R. / Wu, Y. / Fang, C. / Zhou, X. / Jiao, J. / Gu, Y. / Zhou, H. / Xie, Z. / Sun, Z. / Chen, D. / Dai, K. / Wang, D. / Tang, W. / Yang, T.T.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 242.9 KB | Display | ![]() |
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PDB format | ![]() | 192.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ggsS S: Starting model for refinement |
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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
#1: Antibody | Mass: 23275.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Antibody | Mass: 23447.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#3: Protein | Mass: 15954.713 Da / Num. of mol.: 1 / Mutation: C93S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() Variant (production host): BL21 / References: UniProt: Q15116 | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.78 % / Description: single long shape |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2M NaCl , 0.1M Tris pH 8, 14% PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: May 6, 2019 / Details: Q315r |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→41.9 Å / Num. obs: 62244 / % possible obs: 98.2 % / Redundancy: 10 % / CC1/2: 0.994 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.053 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 7 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2532 / CC1/2: 0.796 / Rrim(I) all: 0.421 / % possible all: 80.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GGS Resolution: 1.7→41.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.339 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.105 / 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: 16.745 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→41.9 Å
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Refine LS restraints |
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