+Open data
-Basic information
Entry | Database: PDB / ID: 6umu | ||||||
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Title | Human apo PD-1 triple mutant | ||||||
Components | Programmed cell death protein 1 | ||||||
Keywords | IMMUNE SYSTEM / PD-1 / immune checkpoint | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.183 Å | ||||||
Authors | Tang, S. / Kim, P.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery. Authors: Tang, S. / Kim, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6umu.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6umu.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 6umu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6umu_validation.pdf.gz | 251.2 KB | Display | wwPDB validaton report |
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Full document | 6umu_full_validation.pdf.gz | 251.1 KB | Display | |
Data in XML | 6umu_validation.xml.gz | 1.1 KB | Display | |
Data in CIF | 6umu_validation.cif.gz | 3.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/6umu ftp://data.pdbj.org/pub/pdb/validation_reports/um/6umu | HTTPS FTP |
-Related structure data
Related structure data | 6umtC 6umvC 3rrqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14513.199 Da / Num. of mol.: 1 / Fragment: UNP residues 33-150 / Mutation: N74G, T76P, A132V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116 | ||||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium chloride, 100 mM Tris-HCl, pH 8.0, 27% w/v PEG5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.18→50 Å / Num. obs: 36705 / % possible obs: 99.8 % / Redundancy: 10 % / Biso Wilson estimate: 16.72 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.017 / Rrim(I) all: 0.056 / Χ2: 1.826 / Net I/σ(I): 11.9 / Num. measured all: 365601 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3RRQ Resolution: 1.183→36.493 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.11 Å2 / Biso mean: 23.7131 Å2 / Biso min: 9.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.183→36.493 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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