- PDB-6dhb: Crystal structure of the human TIM-3 with bound Calcium -
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Basic information
Entry
Database: PDB / ID: 6dhb
Title
Crystal structure of the human TIM-3 with bound Calcium
Components
Hepatitis A virus cellular receptor 2
Keywords
IMMUNE SYSTEM / T Cell Immunoglobulin Mucin-3 Immunological tolerance
Function / homology
Function and homology information
regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of T-helper 1 type immune response / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of defense response to bacterium / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / toll-like receptor 7 signaling pathway ...regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of T-helper 1 type immune response / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of defense response to bacterium / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / toll-like receptor 7 signaling pathway / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / negative regulation of immunological synapse formation / positive regulation of interleukin-1 production / toll-like receptor 3 signaling pathway / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / toll-like receptor 9 signaling pathway / mediator complex / macrophage activation involved in immune response / positive regulation of macrophage activation / anchoring junction / negative regulation of interleukin-2 production / positive regulation of interleukin-4 production / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / immunological synapse / maternal process involved in female pregnancy / negative regulation of T cell proliferation / positive regulation of T cell proliferation / positive regulation of chemokine production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cellular response to lipopolysaccharide / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / early endosome / defense response to Gram-positive bacterium / inflammatory response / negative regulation of gene expression / innate immune response / regulation of transcription by RNA polymerase II / cell surface / metal ion binding Similarity search - Function
Resolution: 1.7→33.09 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.665 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18054
528
4.9 %
RANDOM
Rwork
0.15024
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obs
0.15174
10256
99.13 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å