Annotations: 9HUJ

CryoEM structure of human peptidylarginine deiminase type 4 (PAD4) in complex with heparin oligomer (12 subunits)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D	SCOP2B Superfamily	Cupredoxins	8039685	3000886	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Peptidylarginine deiminase Pad4, middle domain	8039684	3000247	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Pentein	8039686	3000640	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cupredoxins	8039685	3000886	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Pentein	8039686	3000640	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Peptidylarginine deiminase Pad4, middle domain	8039684	3000247	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pentein	8039686	3000640	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cupredoxins	8039685	3000886	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Pentein	8039686	3000640	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Peptidylarginine deiminase Pad4, middle domain	8039684	3000247	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cupredoxins	8039685	3000886	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)
D	RVT_1	e9hujD1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: RVT_1	ECOD (v295.2)
C	PAD_N	e9hujC1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: PAD_N	ECOD (v295.2)
C	RVT_1	e9hujC2	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: RVT_1	ECOD (v295.2)
B	PAD_N	e9hujB1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: PAD_N	ECOD (v295.2)
A	PAD_N	e9hujA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: PAD_N	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, B, C, D	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, B, C, D	Protein-arginine deiminase type-4	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 H3R8 arginine deiminase activity 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 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 H3R8 arginine deiminase activity 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 histone H3R2 arginine deiminase activity histone H3R17 arginine deiminase activity identical protein binding protein binding	regulation of cellular process regulation of cellular component organization negative regulation of heterochromatin formation positive regulation of biological process negative regulation of biological process negative regulation of chromatin organization positive regulation of macromolecule biosynthetic process cellular component organization cellular component biogenesis positive regulation of metabolic process cellular component assembly positive regulation of biosynthetic process chromatin organization negative regulation of cellular process regulation of cellular process regulation of cellular component organization negative regulation of heterochromatin formation positive regulation of biological process negative regulation of biological process negative regulation of chromatin organization positive regulation of macromolecule biosynthetic process cellular component organization cellular component biogenesis positive regulation of metabolic process cellular component assembly positive regulation of biosynthetic process chromatin organization negative regulation of cellular process chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biosynthetic process regulation of biological process heterochromatin formation regulation of chromatin organization negative regulation of cellular component organization epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process heterochromatin organization gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process positive regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of heterochromatin organization regulation of macromolecule biosynthetic process metabolic process cellular process negative regulation of gene expression, epigenetic macromolecule metabolic process negative regulation of heterochromatin organization regulation of metabolic process macromolecule modification primary metabolic process protein metabolic process protein modification process neutrophil extracellular trap formation membrane organization cellular component disassembly nuclear membrane disassembly membrane disassembly nuclear membrane organization nucleus organization organelle organization nuclear envelope organization endomembrane system organization protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization protein-containing complex assembly nucleosome assembly nucleosome organization post-translational protein modification developmental process multicellular organismal process maintenance of cell number stem cell population maintenance	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	: Q9UM07	rheumatoid arthritis Mammary Neoplasms, Experimental sarcomatoid carcinoma carcinoma skin basal cell carcinoma osteosarcoma tuberculosis mammary neoplasms, animal psoriasis schizophrenia undifferentiated carcinoma