5GQD | pdb_00005gqd

Crystal structure of covalent glycosyl-enzyme intermediate of xylanase mutant (T82A, N127S, and E128H) from Streptomyces olivaceoviridis E-86

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)
B	d5gqdb2	All beta proteins	beta-Trefoil	Ricin B-like lectins	automated matches	automated matches	(Streptomyces olivaceoviridis ) [TaxId: 1921 ],	SCOPe (2.08)
B	d5gqdb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	automated matches	(Streptomyces olivaceoviridis ) [TaxId: 1921 ],	SCOPe (2.08)
A	d5gqda2	All beta proteins	beta-Trefoil	Ricin B-like lectins	automated matches	automated matches	(Streptomyces olivaceoviridis ) [TaxId: 1921 ],	SCOPe (2.08)
A	d5gqda1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	automated matches	(Streptomyces olivaceoviridis ) [TaxId: 1921 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	(Trans)glycosidases	8035532	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ricin B-like lectins	8035529	3000678	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ricin B-like lectins	8035529	3000678	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8035532	3000313	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)
B	Ricin_B_lectin	e5gqdB1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Ricin_B_lectin	ECOD (1.6)
B	Glyco_hydro_10	e5gqdB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_10	ECOD (1.6)
A	Ricin_B_lectin	e5gqdA2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Ricin_B_lectin	ECOD (1.6)
A	Glyco_hydro_10	e5gqdA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_10	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
B	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00331	Glycosyl hydrolase family 10 (Glyco_hydro_10)	Glycosyl hydrolase family 10		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Beta-xylanase	xylanase activity hydrolase activity, acting on glycosyl bonds endo-1,4-beta-xylanase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity	carbohydrate metabolic process xylan catabolic process catabolic process carbohydrate catabolic process hemicellulose catabolic process primary metabolic process macromolecule catabolic process xylan metabolic process polysaccharide metabolic process polysaccharide catabolic process metabolic process cellular process macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR044846	Glycoside hydrolase family 10	Family
A, B	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B	IPR035992	Ricin B-like lectins	Homologous Superfamily
A, B	IPR001000	Glycoside hydrolase family 10 domain	Domain
A, B	IPR031158	Glycosyl hydrolases family 10, active site	Active Site
A, B	IPR000772	Ricin B, lectin domain	Domain

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.