4ATF | pdb_00004atf

Crystal structure of inactivated mutant beta-agarase B in complex with agaro-octaose

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)
D	d4atfd1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Glycosyl hydrolases family 16	automated matches	(Zobellia galactanivorans ) [TaxId: 63186 ],	SCOPe (2.08)
D	d4atfd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Zobellia galactanivorans ) [TaxId: 63186 ],	SCOPe (2.08)
C	d4atfc1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Glycosyl hydrolases family 16	automated matches	(Zobellia galactanivorans ) [TaxId: 63186 ],	SCOPe (2.08)
C	d4atfc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Zobellia galactanivorans ) [TaxId: 63186 ],	SCOPe (2.08)
B	d4atfb_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Glycosyl hydrolases family 16	automated matches	(Zobellia galactanivorans ) [TaxId: 63186 ],	SCOPe (2.08)
A	d4atfa_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Glycosyl hydrolases family 16	automated matches	(Zobellia galactanivorans ) [TaxId: 63186 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8061260	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8061260	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8061260	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8061260	3000120	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)
D	SmpA_OmlA	e4atfD1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
C	SmpA_OmlA	e4atfC1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
B	SmpA_OmlA	e4atfB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
A	EF-hand_1,S_100	e4atfA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: SH3	T: SH3	F: EF-hand_1,S_100	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
A	2.60.120.200	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	PF00722	Glycosyl hydrolases family 16 (Glyco_hydro_16)	Glycosyl hydrolases family 16		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	BETA-AGARASE B	hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity beta-agarase activity catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	carbohydrate metabolic process primary metabolic process metabolic process cellular process	cell outer membrane cellular anatomical structure external encapsulating structure extracellular region membrane cell envelope outer membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B, C, D	IPR000757	Beta-glucanase-like, N-terminal domain	Domain
A, B, C, D	IPR016287	Beta-agarase	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.