6JTJ | pdb_00006jtj

Crystal structure of NagZ from Neisseria gonorrhoeae in complex with N-acetylglucosamine

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	(Trans)glycosidases	8099582	3000313	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	(Trans)glycosidases	8099582	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Trans)glycosidases	8099582	3000313	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Trans)glycosidases	8099582	3000313	SCOP2B (2022-06-29)
B	SCOP2 Family	NagZ-like	8099581	4003202	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	(Trans)glycosidases	8099582	3000313	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8099582	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)
E	C1-set	e6jtjE1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
F	C1-set	e6jtjF1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
D	C1-set	e6jtjD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
C	C1-set	e6jtjC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
B	C1-set	e6jtjB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
A	C1-set	e6jtjA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.20.20.300	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycoside hydrolase, family 3, N-terminal domain	CATH (utative)
F	3.20.20.300	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycoside hydrolase, family 3, N-terminal domain	CATH (utative)
D	3.20.20.300	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycoside hydrolase, family 3, N-terminal domain	CATH (utative)
C	3.20.20.300	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycoside hydrolase, family 3, N-terminal domain	CATH (utative)
B	3.20.20.300	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycoside hydrolase, family 3, N-terminal domain	CATH (utative)
A	3.20.20.300	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycoside hydrolase, family 3, N-terminal domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00933	Glycosyl hydrolase family 3 N terminal domain (Glyco_hydro_3)	Glycosyl hydrolase family 3 N terminal domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Beta-hexosaminidase	hydrolase activity, acting on glycosyl bonds hexosaminidase activity beta-N-acetylhexosaminidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis carbohydrate metabolic process primary metabolic process metabolic process developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis carbohydrate metabolic process primary metabolic process metabolic process cellular process cell division cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process glycosaminoglycan biosynthetic process macromolecule metabolic process cell wall macromolecule metabolic process peptidoglycan turnover	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR001764	Glycoside hydrolase, family 3, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR022956	Beta-hexosaminidase, bacterial	Family
A, B, C, D, E A, B, C, D, E, F	IPR036962	Glycoside hydrolase, family 3, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR050226	NagZ Beta-hexosaminidase	Family
A, B, C, D, E A, B, C, D, E, F	IPR019800	Glycoside hydrolase, family 3, active site	Active Site

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.