3EIJ | pdb_00003eij

Crystal structure of Pdcd4

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	ARM repeat-like	8086320	3000116	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8086320	3000116	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PGM_PMM_I	e3eijB3	A: alpha bundles	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase	T: Glutamine synthetase/guanido kinase	F: PGM_PMM_I	ECOD (develop294)
A	Xpo1,Exportin-T	e3eijA3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Xpo1,Exportin-T	ECOD (develop294)
A	FTO_NTD	e3eijA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: FTO_NTD	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.25.40.180	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.25.40.180	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02847	MA3 domain (MA3)	MA3 domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Programmed cell death protein 4	RNA binding binding nucleic acid binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular response to stimulus cellular response to BMP stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus cell communication cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway signal transduction response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway regulation of catalytic activity negative regulation of catalytic activity regulation of signal transduction regulation of transferase activity regulation of MAP kinase activity intracellular signal transduction negative regulation of kinase activity negative regulation of JNK cascade JNK cascade phosphate-containing compound metabolic process intracellular signaling cassette negative regulation of protein modification process phosphorus metabolic process protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process regulation of JNK cascade regulation of MAPK cascade regulation of molecular function regulation of kinase activity regulation of response to stimulus negative regulation of protein phosphorylation regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of phosphate metabolic process negative regulation of cell communication regulation of intracellular signal transduction negative regulation of protein serine/threonine kinase activity protein metabolic process negative regulation of JUN kinase activity regulation of signaling negative regulation of response to stimulus negative regulation of molecular function negative regulation of MAP kinase activity regulation of protein kinase activity negative regulation of protein kinase activity negative regulation of signal transduction negative regulation of phosphorus metabolic process regulation of JUN kinase activity MAPK cascade regulation of cell communication regulation of phosphorylation negative regulation of phosphorylation negative regulation of MAPK cascade regulation of defense response regulation of response to external stimulus defense response positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus 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 multicellular organismal process cellular developmental process heart morphogenesis cell development mesenchyme development epicardium-derived cardiac fibroblast cell differentiation multicellular organism development cardiac fibroblast cell development cell differentiation anatomical structure development cardiac epithelial to mesenchymal transition animal organ morphogenesis cardiac cell development system development developmental process heart development cardiac fibroblast cell differentiation animal organ development tissue development cardiocyte differentiation epithelial to mesenchymal transition involved in cardiac fibroblast development circulatory system development epithelial to mesenchymal transition anatomical structure morphogenesis epicardium-derived cardiac fibroblast cell development mesenchymal cell differentiation positive regulation of endothelial cell apoptotic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process endothelial cell apoptotic process apoptotic process programmed cell death regulation of endothelial cell apoptotic process positive regulation of cellular process positive regulation of cell communication positive regulation of signal transduction regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction positive regulation of non-canonical NF-kappaB signal transduction positive regulation of signaling smooth muscle cell differentiation regulation of developmental process regulation of smooth muscle cell differentiation negative regulation of muscle cell differentiation regulation of cell differentiation muscle cell differentiation muscle structure development vascular associated smooth muscle cell differentiation negative regulation of cell differentiation negative regulation of developmental process negative regulation of vascular associated smooth muscle cell differentiation regulation of vascular associated smooth muscle cell differentiation vasculature development negative regulation of smooth muscle cell differentiation regulation of muscle cell differentiation biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin regulation of myofibroblast differentiation myofibroblast differentiation negative regulation of myofibroblast differentiation muscle cell apoptotic process positive regulation of smooth muscle cell apoptotic process smooth muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of smooth muscle cell apoptotic process positive regulation of muscle cell apoptotic process vascular associated smooth muscle cell apoptotic process positive regulation of vascular associated smooth muscle cell apoptotic process regulation of vascular associated smooth muscle cell apoptotic process regulation of vascular associated smooth muscle cell proliferation negative regulation of cell population proliferation cell population proliferation regulation of smooth muscle cell proliferation negative regulation of vascular associated smooth muscle cell proliferation smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation regulation of cytokine production involved in inflammatory response cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response negative regulation of cytokine production cytokine production involved in inflammatory response negative regulation of gene expression negative regulation of multicellular organismal process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR039778	Programmed cell death protein 4	Family
A, B	IPR003891	Initiation factor eIF-4 gamma, MA3	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q53EL6	Neoplasm Invasiveness cancer ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis adrenal cortex carcinoma tuberculosis esophageal adenocarcinoma lung lymphangioleiomyomatosis lymphangioma malignant ependymoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia renal cell carcinoma Neoplasm Invasiveness cancer ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis adrenal cortex carcinoma tuberculosis esophageal adenocarcinoma lung lymphangioleiomyomatosis lymphangioma malignant ependymoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia renal cell carcinoma atrial fibrillation tuberous sclerosis lung adenocarcinoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor ulcerative colitis disappearing bone disease lung benign neoplasm malignant colon neoplasm

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.