4N2D

Crystal structure of Protein Arginine Deiminase 2 (D123N, 0 mM Ca2+)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4n2da2	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Peptidylarginine deiminase Pad4, middle domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4n2da1	All beta proteins	Cupredoxin-like	Cupredoxins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4n2da3	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4n2da4	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PAD_M	e4n2dA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: PAD_M	ECOD (1.6)
A	PAD_N	e4n2dA1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: PAD_N	ECOD (1.6)
A	PAD	e4n2dA4	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: PAD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.1860	Mainly Beta	Sandwich	Immunoglobulin-like	Protein-arginine deiminase, N-terminal domain	CATH (4.3.0)
A	2.60.40.1700	Mainly Beta	Sandwich	Immunoglobulin-like	Protein-arginine deiminase, central domain	CATH (4.3.0)
A	3.75.10.10	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08527	Protein-arginine deiminase (PAD) middle domain (PAD_M)	Protein-arginine deiminase (PAD) middle domain	This family represents the central non-catalytic domain of protein-arginine deiminase. This domain has an immunoglobulin-like fold.	Domain
A	PF03068	Protein-arginine deiminase (PAD) (PAD)	Protein-arginine deiminase (PAD)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Protein-arginine deiminase type-2	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding histone H3 arginine deiminase activity catalytic activity, acting on a protein histone arginine deiminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines hydrolase activity histone modifying activity protein-arginine deiminase activity catalytic activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding histone H3 arginine deiminase activity catalytic activity, acting on a protein histone arginine deiminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines hydrolase activity histone modifying activity protein-arginine deiminase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone H3R26 arginine deiminase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear estrogen receptor binding	regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process cellular response to stimulus response to stimulus negative regulation of signaling signaling regulation of chemokine-mediated signaling pathway negative regulation of biological process response to cytokine response to chemokine regulation of signal transduction negative regulation of cell communication cytokine-mediated signaling pathway cellular response to chemokine negative regulation of G protein-coupled receptor signaling pathway cell communication chemokine-mediated signaling pathway negative regulation of cellular process cellular response to cytokine stimulus signal transduction regulation of G protein-coupled receptor signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cytokine-mediated signaling pathway negative regulation of chemokine-mediated signaling pathway negative regulation of signal transduction response to peptide regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus negative regulation of cytokine-mediated signaling pathway response to chemical regulation of cell communication G protein-coupled receptor signaling pathway negative regulation of mononuclear cell migration negative regulation of locomotion regulation of cell motility negative regulation of chemotaxis regulation of lymphocyte chemotaxis taxis cell migration regulation of immune system process negative regulation of lymphocyte migration regulation of mononuclear cell migration negative regulation of cell migration chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration lymphocyte migration response to external stimulus leukocyte migration negative regulation of leukocyte migration regulation of locomotion negative regulation of response to external stimulus negative regulation of cell motility negative regulation of leukocyte chemotaxis regulation of response to external stimulus lymphocyte chemotaxis regulation of lymphocyte migration regulation of cell migration negative regulation of lymphocyte chemotaxis cell motility locomotion cell chemotaxis regulation of chemotaxis cellular response to chemical stimulus negative regulation of immune system process immune system process mononuclear cell migration leukocyte chemotaxis developmental process multicellular organismal process head development animal organ development brain development nervous system development substantia nigra development multicellular organism development central nervous system development midbrain development anatomical structure development neural nucleus development system development intracellular receptor signaling pathway response to lipid hormone-mediated signaling pathway intracellular signal transduction cellular response to endogenous stimulus response to hormone response to steroid hormone nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus response to organic cyclic compound steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus cellular response to organic cyclic compound estrogen receptor signaling pathway cellular response to lipid nuclear receptor-mediated signaling pathway response to leukemia inhibitory factor cellular response to leukemia inhibitory factor	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol lytic vacuole extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol lytic vacuole intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen vacuolar lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle lysosome vesicle lumen azurophil granule vacuole intracellular membrane-bounded organelle secretory granule lumen azurophil granule lumen organelle lumen secretory granule primary lysosome secretory vesicle euchromatin membraneless organelle intracellular membraneless organelle chromatin chromosome nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013732	Protein-arginine deiminase (PAD), N-terminal	Domain
A	IPR013733	Protein-arginine deiminase (PAD), central domain	Domain
A	IPR008972	Cupredoxin	Homologous Superfamily
A	IPR038685	PAD, N-terminal domain superfamily	Homologous Superfamily
A	IPR013530	Protein-arginine deiminase, C-terminal	Domain
A	IPR036556	Protein-arginine deiminase, central domain superfamily	Homologous Superfamily
A	IPR004303	Protein-arginine deiminase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9Y2J8	atypical teratoid rhabdoid tumor Crohn disease lung cancer malignant pancreatic neoplasm primitive neuroectodermal tumor schizophrenia breast cancer exocrine pancreatic carcinoma malignant colon neoplasm medulloblastoma psoriasis tuberculosis chronic obstructive pulmonary disease large cell medulloblastoma malignant ependymoma atypical teratoid rhabdoid tumor Crohn disease lung cancer malignant pancreatic neoplasm primitive neuroectodermal tumor schizophrenia breast cancer exocrine pancreatic carcinoma malignant colon neoplasm medulloblastoma psoriasis tuberculosis chronic obstructive pulmonary disease large cell medulloblastoma malignant ependymoma osteosarcoma rheumatoid arthritis ulcerative colitis

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.