3GXK | pdb_00003gxk

The crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Native structure to 1.9

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d3gxkd_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	G-type lysozyme	automated matches	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
C	d3gxkc_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	G-type lysozyme	automated matches	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
B	d3gxkb_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	G-type lysozyme	automated matches	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)
A	d3gxka_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	G-type lysozyme	automated matches	Atlantic cod (Gadus morhua ) [TaxId: 8049 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Lysozyme-like	8069409	3001879	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lysozyme-like	8069409	3001879	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lysozyme-like	8069409	3001879	SCOP2B (2022-06-29)
A	SCOP2 Family	G-type lysozyme	8069408	4000899	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Lysozyme-like	8069409	3001879	SCOP2 (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	PDEase_I	e3gxkD1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
C	PDEase_I	e3gxkC1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
B	PDEase_I	e3gxkB1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
A	PilS	e3gxkA1	A: alpha bundles	X: Cystatin-like	H: Cupredoxin-related	T: Cupredoxin-related	F: PilS	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Provenance Source (Version)
D	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme	CATH (4.3.0)
C	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme	CATH (4.3.0)
B	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme	CATH (4.3.0)
A	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Goose-type lysozyme 1	hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity	carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process cellular process macromolecule metabolic process biological process involved in interspecies interaction between organisms carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process cellular process macromolecule metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to Gram-positive bacterium response to external stimulus response to biotic stimulus defense response to bacterium response to bacterium response to stress response to external biotic stimulus disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002152	Glycoside hydrolase, family 23	Family
A, B, C, D	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily

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.

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