- PDB-5irn: Crystal structure of rabbit NOD2 in an ADP-bound state (Crystal form1) -
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Basic information
Entry
Database: PDB / ID: 5irn
Title
Crystal structure of rabbit NOD2 in an ADP-bound state (Crystal form1)
Components
Uncharacterized protein
Keywords
IMMUNE SYSTEM / NOD2 / innate immunity
Function / homology
Function and homology information
biosynthetic process of antibacterial peptides active against Gram-positive bacteria / detection of muramyl dipeptide / muramyl dipeptide binding / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / negative regulation of T cell mediated immunity / regulation of neutrophil chemotaxis / negative regulation of interleukin-18 production / positive regulation of dendritic cell antigen processing and presentation / host-mediated regulation of intestinal microbiota composition / intestinal stem cell homeostasis ...biosynthetic process of antibacterial peptides active against Gram-positive bacteria / detection of muramyl dipeptide / muramyl dipeptide binding / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / negative regulation of T cell mediated immunity / regulation of neutrophil chemotaxis / negative regulation of interleukin-18 production / positive regulation of dendritic cell antigen processing and presentation / host-mediated regulation of intestinal microbiota composition / intestinal stem cell homeostasis / negative regulation of toll-like receptor 2 signaling pathway / regulation of appetite / toll-like receptor 2 signaling pathway / negative regulation of macrophage cytokine production / negative regulation of macrophage apoptotic process / positive regulation of humoral immune response mediated by circulating immunoglobulin / antibacterial innate immune response / maintenance of gastrointestinal epithelium / positive regulation of mitophagy / positive regulation of xenophagy / xenophagy / positive regulation of B cell activation / positive regulation of type 2 immune response / positive regulation of protein K63-linked ubiquitination / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / cellular response to peptidoglycan / peptidoglycan binding / negative regulation of interleukin-12 production / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of cytokine production involved in inflammatory response / positive regulation of monocyte chemotactic protein-1 production / positive regulation of macrophage cytokine production / pattern recognition receptor activity / negative regulation of interleukin-2 production / temperature homeostasis / extrinsic component of plasma membrane / positive regulation of Notch signaling pathway / response to exogenous dsRNA / positive regulation of interleukin-17 production / positive regulation of nitric-oxide synthase biosynthetic process / response to muramyl dipeptide / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / phagocytosis / detection of bacterium / stress-activated MAPK cascade / positive regulation of phagocytosis / JNK cascade / negative regulation of inflammatory response to antigenic stimulus / Hsp70 protein binding / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / phagocytic vesicle / response to endoplasmic reticulum stress / innate immune response in mucosa / positive regulation of interleukin-1 beta production / ubiquitin binding / positive regulation of interleukin-8 production / positive regulation of epithelial cell proliferation / establishment of localization in cell / positive regulation of JNK cascade / Hsp90 protein binding / ADP binding / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / actin binding / basolateral plasma membrane / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / defense response to bacterium / protein-containing complex binding / protein kinase binding / Golgi apparatus / cell surface / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / ATP binding / cytosol Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.3→92.7 Å / Num. obs: 57510 / % possible obs: 92.6 % / Redundancy: 6.7 % / Net I/σ(I): 29.7
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0103
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
phasing
Refinement
Resolution: 2.34→92.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.943 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23585
3063
5.1 %
RANDOM
Rwork
0.20155
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obs
0.20329
57509
91.77 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å