4YT9 | pdb_00004yt9

Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) substrate-unbound.

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4yt9A1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F:	ECOD (v294.1)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	Peptidylarginine 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	polyamine metabolic process putrescine biosynthetic process amine metabolic process biogenic amine biosynthetic process biosynthetic process amine biosynthetic process polyamine biosynthetic process putrescine metabolic process metabolic process cellular process biogenic amine metabolic process	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007466	Peptidyl-arginine deiminase, Porphyromonas-type	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	4GJ	Parent Component: CYS
A	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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.