6NIC

Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-aminohexanamide

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6nica_	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	Porphyromonas-type peptidylarginine deiminase	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	SCOPe (2.08)
B	d6nicb_	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	Porphyromonas-type peptidylarginine deiminase	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	SCOPe (2.08)
C	d6nicc_	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	Porphyromonas-type peptidylarginine deiminase	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	SCOPe (2.08)
D	d6nicd_	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	Porphyromonas-type peptidylarginine deiminase	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	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	8094641	3000640	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pentein	8094641	3000640	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Pentein	8094641	3000640	SCOP2B (2022-06-29)
D	SCOP2 Family	Porphyromonas-type peptidylarginine deiminase	8094640	4002769	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Pentein	8094641	3000640	SCOP2 (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_porph	e6nicA1	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: PAD_porph	ECOD (1.6)
B	PAD_porph	e6nicB1	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: PAD_porph	ECOD (1.6)
C	PAD_porph	e6nicC1	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: PAD_porph	ECOD (1.6)
D	PAD_porph	e6nicD1	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: PAD_porph	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.75.10.10	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (4.3.0)
B	3.75.10.10	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (4.3.0)
C	3.75.10.10	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (4.3.0)
D	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, B, C, D	PF04371	Porphyromonas-type peptidyl-arginine deiminase (PAD_porph)	Porphyromonas-type peptidyl-arginine deiminase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Porphyromonas-type peptidyl-arginine deiminase	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines hydrolase activity protein-arginine deiminase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds agmatine deiminase activity	oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process polyamine metabolic process alpha-amino acid metabolic process arginine metabolic process putrescine biosynthetic process amine metabolic process biogenic amine biosynthetic process biosynthetic process amine biosynthetic process polyamine biosynthetic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process polyamine metabolic process alpha-amino acid metabolic process arginine metabolic process putrescine biosynthetic process amine metabolic process biogenic amine biosynthetic process biosynthetic process amine biosynthetic process polyamine biosynthetic process putrescine biosynthetic process from arginine putrescine metabolic process metabolic process small molecule metabolic process cellular process biogenic amine metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR007466	Peptidyl-arginine deiminase, Porphyromonas-type	Family
A, B, C, D	IPR017754	Agmatine deiminase	Family

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.