3KS7

Crystal structure of Putative Peptide:N-glycosidase F (PNGase F) (YP_210507.1) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	N-glycanase_C	e3ks7A2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: N-glycanase_C	ECOD (1.6)
A	N-glycanase_N	e3ks7A3	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: N-glycanase_N	ECOD (1.6)
B	N-glycanase_C	e3ks7B2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: N-glycanase_C	ECOD (1.6)
B	N-glycanase_N	e3ks7B1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: N-glycanase_N	ECOD (1.6)
D	N-glycanase_C	e3ks7D2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: N-glycanase_C	ECOD (1.6)
D	N-glycanase_N	e3ks7D1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: N-glycanase_N	ECOD (1.6)
C	N-glycanase_C	e3ks7C2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: N-glycanase_C	ECOD (1.6)
C	N-glycanase_N	e3ks7C1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: N-glycanase_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.1570	Mainly Beta	Sandwich	Jelly Rolls	Peptide-N-glycosidase F, N-terminal domain	CATH (4.3.0)
A	2.60.120.230	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.60.120.1570	Mainly Beta	Sandwich	Jelly Rolls	Peptide-N-glycosidase F, N-terminal domain	CATH (4.3.0)
B	2.60.120.230	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	2.60.120.1570	Mainly Beta	Sandwich	Jelly Rolls	Peptide-N-glycosidase F, N-terminal domain	CATH (4.3.0)
D	2.60.120.230	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.60.120.1570	Mainly Beta	Sandwich	Jelly Rolls	Peptide-N-glycosidase F, N-terminal domain	CATH (4.3.0)
C	2.60.120.230	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF09113	Peptide-N-glycosidase F, C terminal (N-glycanase_C)	Peptide-N-glycosidase F, C terminal	Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The doma ...	Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins [1].	Domain
A, B, C, D	PF09112	Peptide-N-glycosidase F, N terminal (N-glycanase_N)	Peptide-N-glycosidase F, N terminal	Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The doma ...	Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Putative Putative PNGase F	oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity hydrolase activity, acting on glycosyl bonds hydrolase activity	metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR008977	PHM/PNGase F domain superfamily	Homologous Superfamily
A, B, C, D	IPR015197	Peptide-N-glycosidase F, C-terminal	Domain
A, B, C, D	IPR014784	Copper type II, ascorbate-dependent monooxygenase-like, C-terminal	Homologous Superfamily
A, B, C, D	IPR043022	Peptide-N-glycosidase F, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR015196	Peptide-N-glycosidase F, N-terminal	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.