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Open data
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Basic information
Entry | Database: PDB / ID: 6j14 | ||||||
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Title | Complex structure of GY-14 and PD-1 | ||||||
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![]() | IMMUNE SYSTEM / tumor immunotherapy / complex structure / FG loop | ||||||
Function / homology | ![]() negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response / PD-1 signaling / adaptive immune response ...negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response / PD-1 signaling / adaptive immune response / Potential therapeutics for SARS / external side of plasma membrane / apoptotic process / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, D. / Tan, S. / Whang, H. / Zhang, H. / Chai, Y. / Qi, J. / Yan, J. / Gao, G.F. | ||||||
![]() | ![]() Title: The FG Loop of PD-1 Serves as a "Hotspot" for Therapeutic Monoclonal Antibodies in Tumor Immune Checkpoint Therapy. Authors: Chen, D. / Tan, S. / Zhang, H. / Wang, H. / He, W. / Shi, R. / Tong, Z. / Zhu, J. / Cheng, H. / Gao, S. / Chai, Y. / Qi, J. / Xiao, M. / Yan, J. / Gao, G.F. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.4 KB | Display | ![]() |
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PDB format | ![]() | 65 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.9 KB | Display | ![]() |
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Full document | ![]() | 453.8 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j15C ![]() 3eyqS ![]() 3rrqS 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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1 |
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Unit cell |
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Components
#1: Antibody | Mass: 13149.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() |
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#2: Antibody | Mass: 12421.966 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() |
#3: Protein | Mass: 12887.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: Q15116 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.82 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 6.5 Details: 0.06 M MgCl2, CaCl2, 0.1 M imidazole-MES (pH 6.5), 18% v/v ethylene glycol and polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 66956 / % possible obs: 97.07 % / Redundancy: 7 % / Net I/σ(I): 7.69 |
Reflection shell | Resolution: 1.4→1.45 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3RRQ,3EYQ Resolution: 1.4→44.032 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→44.032 Å
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Refine LS restraints |
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LS refinement shell |
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