4DKT | pdb_00004dkt

Crystal structure of human peptidylarginine deiminase 4 in complex with N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2-fluoroethanimidoyl]-L-ornithinamide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4dkta2	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Peptidylarginine deiminase Pad4, middle domain	Peptidylarginine deiminase Pad4, middle domain	Peptidylarginine deiminase Pad4, middle domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4dkta1	All beta proteins	Cupredoxin-like	Cupredoxins	Peptidylarginine deiminase Pad4, N-terminal domain	Peptidylarginine deiminase Pad4, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4dkta3	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	Peptidylarginine deiminase Pad4, catalytic C-terminal domain	Peptidylarginine deiminase Pad4, catalytic C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Pentein	8039686	3000640	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cupredoxins	8039685	3000886	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Peptidylarginine deiminase Pad4, middle domain	8039684	3000247	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)
A	PAD_M	e4dktA1	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	e4dktA3	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: PAD_N	ECOD (1.6)
A	PAD	e4dktA2	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-4	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding histone H2AR3 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 H2AR3 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 H3 arginine deiminase activity histone H3R8 arginine deiminase activity histone H3R26 arginine deiminase activity histone H3R2 arginine deiminase activity histone H3R17 arginine deiminase activity histone H4R3 arginine deiminase activity histone H1R54 arginine deiminase activity identical protein binding protein binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular component organization or biogenesis 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
B	Thr-Asp-F-amidine	-	-	-

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: Q9UM07	rheumatoid arthritis Mammary Neoplasms, Experimental sarcomatoid carcinoma carcinoma skin basal cell carcinoma osteosarcoma tuberculosis mammary neoplasms, animal psoriasis schizophrenia undifferentiated carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
B	FIO	Parent Component: ARG RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354
B	NH2	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359 , L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

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.