3PVQ | pdb_00003pvq

Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution

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)
B	N-glycanase_C	e3pvqB7	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: N-glycanase_C	ECOD (v294.1)
A	N-glycanase_C	e3pvqA7	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: N-glycanase_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
B	3.90.1720.10	Alpha Beta	Alpha-Beta Complex	endopeptidase fold (from Nostoc punctiforme)	endopeptidase domain like (from Nostoc punctiforme)	CATH (4.3.0)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
A	3.90.1720.10	Alpha Beta	Alpha-Beta Complex	endopeptidase fold (from Nostoc punctiforme)	endopeptidase domain like (from Nostoc punctiforme)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00877	NlpC/P60 family (NLPC_P60)	NlpC/P60 family	The function of this domain is unknown. It is found in several lipoproteins.	Domain
A, B	PF18348	Bacterial dipeptidyl-peptidase Sh3 domain (SH3_16)	Bacterial dipeptidyl-peptidase Sh3 domain	This is the first of two N-terminal bacterial SH3 (SH3b) domains found in bacterial dipeptidyl-peptidases VI such as gamma-D-glutamyl-L-diamino acid endopeptidases. The first SH3b domain plays an important role in defining substrate specificity by co ...	This is the first of two N-terminal bacterial SH3 (SH3b) domains found in bacterial dipeptidyl-peptidases VI such as gamma-D-glutamyl-L-diamino acid endopeptidases. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Dipeptidyl-peptidase VI	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity	glycosaminoglycan metabolic process aminoglycan metabolic process peptidoglycan metabolic process carbohydrate derivative metabolic process metabolic process cellular process macromolecule metabolic process proteolysis primary metabolic process protein metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000064	Endopeptidase, NLPC/P60 domain	Domain
A, B	IPR041382	Bacterial dipeptidyl-peptidase SH3 domain	Domain
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR051202	Peptidase C40	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	MSE	Parent Component: MET
A, B	OCS	Parent Component: CYS RESID: AA0556 PSI-MOD : L-cysteic acid (L-cysteine sulfonic acid) MOD:00460

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.