8P6Q | pdb_00008p6q

Racemic structure of TNFR1 cysteine-rich domain

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	TNF receptor-like	8038880	3000971	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00020	TNFR/NGFR cysteine-rich region (TNFR_c6)	TNFR/NGFR cysteine-rich region		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Tumor necrosis factor-binding protein 1	molecular transducer activity signaling receptor activity transmembrane signaling receptor activity tumor necrosis factor receptor activity death receptor activity protein binding binding cytokine binding tumor necrosis factor binding	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular process cellular response to cytokine stimulus cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular process cellular response to cytokine stimulus signal transduction positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling regulation of defense response regulation of response to external stimulus defense response response to external stimulus regulation of inflammatory response positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stress response to stress positive regulation of defense response inflammatory response regulation of lipid metabolic process primary metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of lipid metabolic process metabolic process regulation of metabolic process lipid metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process macromolecule metabolic process negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of canonical NF-kappaB signal transduction negative regulation of cell communication negative regulation of cellular process negative regulation of response to stimulus negative regulation of signal transduction negative regulation of extracellular matrix organization regulation of localization regulation of cellular component organization transport extracellular matrix organization negative regulation of transport cellular component organization localization negative regulation of secretion regulation of secretion by cell secretion by cell negative regulation of secretion by cell cellular component organization or biogenesis regulation of extracellular matrix constituent secretion extracellular structure organization negative regulation of cellular component organization regulation of transport secretion export from cell establishment of localization regulation of secretion negative regulation of extracellular matrix constituent secretion extracellular matrix constituent secretion regulation of extracellular matrix organization external encapsulating structure organization negative regulation of inflammatory response negative regulation of response to external stimulus negative regulation of defense response prostaglandin metabolic process icosanoid metabolic process fatty acid metabolic process unsaturated fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process prostanoid metabolic process small molecule metabolic process monocarboxylic acid metabolic process protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane defense response to bacterium biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external biotic stimulus response to biotic stimulus positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process regulation of execution phase of apoptosis positive regulation of execution phase of apoptosis execution phase of apoptosis apoptotic process programmed cell death developmental process heart development multicellular organismal process heart valve development animal organ development circulatory system development multicellular organism development pulmonary valve development anatomical structure development semi-lunar valve development system development extrinsic apoptotic signaling pathway via death domain receptors extrinsic apoptotic signaling pathway apoptotic signaling pathway protein polyubiquitination protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal cell surface receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT cellular response to stress DNA damage response intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway response to mechanical stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus regulation of establishment of endothelial barrier cellular developmental process regulation of developmental process endothelium development cell development regulation of cell differentiation epithelial cell differentiation regulation of cell development regulation of epithelial cell differentiation endothelial cell development cell differentiation regulation of endothelial cell development regulation of multicellular organismal process epithelium development regulation of multicellular organismal development endothelial cell differentiation regulation of endothelial cell differentiation tissue development epithelial cell development establishment of endothelial barrier cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway response to tumor necrosis factor apoptotic process involved in morphogenesis apoptotic process involved in development positive regulation of developmental process positive regulation of apoptotic process involved in morphogenesis positive regulation of apoptotic process involved in development regulation of apoptotic process involved in development anatomical structure morphogenesis aortic valve development muscle hypertrophy regulation of muscle adaptation system process negative regulation of muscle hypertrophy regulation of system process striated muscle hypertrophy regulation of muscle system process muscle system process regulation of muscle hypertrophy regulation of cardiac muscle hypertrophy muscle adaptation cardiac muscle hypertrophy negative regulation of multicellular organismal process negative regulation of cardiac muscle hypertrophy regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway regulation of response to cytokine stimulus positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription	cellular anatomical structure membrane cell surface cell periphery plasma membrane membrane microdomain membrane raft protein-containing complex receptor complex extracellular region membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus cellular anatomical structure membrane cell surface cell periphery plasma membrane membrane microdomain membrane raft protein-containing complex receptor complex extracellular region membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle cytoplasm organelle membrane tumor necrosis factor receptor superfamily complex extracellular space
B	D-TNFR-1 CRD2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR033993	Tumor necrosis factor receptor 1A, N-terminal	Domain
A	IPR052493	Tumor necrosis factor receptor superfamily member 1A	Family
A	IPR011029	Death-like domain superfamily	Homologous Superfamily
A	IPR020419	Tumour necrosis factor receptor 1A	Family
A	IPR000488	Death domain	Domain
A	IPR001368	TNFR/NGFR cysteine-rich region	Domain
A	IPR033994	Tumor necrosis factor receptor 1A, death domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P19438	autosomal dominant familial periodic fever primary biliary cholangitis multiple sclerosis cystic fibrosis congestive heart failure autoimmune disease Diabetes Mellitus, Experimental amyloidosis allergic disease type 2 diabetes mellitus brain ischemia pneumonia celiac disease malignant ependymoma colorectal adenoma autosomal dominant familial periodic fever primary biliary cholangitis multiple sclerosis cystic fibrosis congestive heart failure autoimmune disease Diabetes Mellitus, Experimental amyloidosis allergic disease type 2 diabetes mellitus brain ischemia pneumonia celiac disease malignant ependymoma colorectal adenoma medulloblastoma Crohn disease ovarian cancer pilocytic astrocytoma acquired metabolic disease pneumonitis schizophrenia arthritic joint disease heart failure intermittent hydrarthrosis brain injury lung carcinoma malignant pancreatic neoplasm colorectal cancer multiple sclerosis, susceptibility to, 5 pancreatic ductal adenocarcinoma pituitary cancer ankylosing spondylitis glioblastoma astrocytic tumor Behcet disease juvenile idiopathic arthritis cancer maturity-onset diabetes of the young depressive disorder periodic fever syndrome exocrine pancreatic carcinoma subependymal giant cell astrocytoma hepatocellular carcinoma large cell medulloblastoma lung cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	DAR
B	DAS	RESID: AA0190 PSI-MOD : D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930
B	DCY	RESID: AA0190
B	DGL	RESID: AA0190
B	DGN	RESID: AA0190
B	DHI	RESID: AA0190
B	DIL	RESID: AA0190 , AA0192 PSI-MOD : D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-allo-isoleucine MOD:00199
B	DLE	RESID: AA0190 , AA0192 , AA0197 PSI-MOD : D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-allo-isoleucine MOD:00199 , D-leucine MOD:00204
B	DLY	RESID: AA0190 , AA0192 , AA0197
B	DPN	RESID: AA0190 , AA0192 , AA0197 , AA0194 PSI-MOD : D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-allo-isoleucine MOD:00199 , D-leucine MOD:00204 , D-phenylalanine MOD:00201
B	DSG	RESID: AA0190 , AA0192 , AA0197 , AA0194 , AA0196 , AA0622 PSI-MOD : D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-allo-isoleucine MOD:00199 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985
B	DSN	RESID: AA0190 , AA0192 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 PSI-MOD : D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-allo-isoleucine MOD:00199 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987
B	DTH	RESID: AA0190 , AA0192 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 , AA0199 PSI-MOD : D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-allo-isoleucine MOD:00199 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987 , D-allo-threonine MOD:00863
B	DTR	RESID: AA0190 , AA0192 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 , AA0199 , AA0198 PSI-MOD : D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-allo-isoleucine MOD:00199 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987 , D-allo-threonine MOD:00863 , D-tryptophan MOD:00205
B	DTY	RESID: AA0190 , AA0192 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 , AA0199 , AA0198
B	DVA	RESID: AA0190 , AA0192 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 , AA0199 , AA0198 , AA0200 PSI-MOD : D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-allo-isoleucine MOD:00199 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987 , D-allo-threonine MOD:00863 , D-tryptophan MOD:00205 , D-valine MOD:00705
B	MED	RESID: AA0190 , AA0192 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 , AA0199 , AA0198 , AA0200 , AA0193 PSI-MOD : D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-allo-isoleucine MOD:00199 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987 , D-allo-threonine MOD:00863 , D-tryptophan MOD:00205 , D-valine MOD:00705 , D-methionine MOD:00200

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.