3G3B | pdb_00003g3b

Structure of a lamprey variable lymphocyte receptor mutant in complex with a protein antigen

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)
H	d3g3bh_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	Lysozyme	bantam,chickens (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
F	d3g3bf_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	Lysozyme	bantam,chickens (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
D	d3g3bd_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	Lysozyme	bantam,chickens (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
B	d3g3bb_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	Lysozyme	bantam,chickens (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
E	d3g3be_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	automated matches	automated matches	Sea Lamprey (Petromyzon marinus ) [TaxId: 7757 ],	SCOPe (2.08)
C	d3g3bc_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	automated matches	automated matches	Sea Lamprey (Petromyzon marinus ) [TaxId: 7757 ],	SCOPe (2.08)
A	d3g3ba_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	automated matches	automated matches	Sea Lamprey (Petromyzon marinus ) [TaxId: 7757 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	SCOP2B (2022-06-29)
E	SCOP2 Family	Ngr ectodomain-like	8047123	4002278	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	L domain-like	8096000	3001010	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	L domain-like	8096000	3001010	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L domain-like	8096000	3001010	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)
H	Lys	e3g3bH1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)
F	Lys	e3g3bF1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)
D	Lys	e3g3bD1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)
B	Lys	e3g3bB1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)
G	LRR_8_1	e3g3bG1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_1	ECOD (1.6)
E	LRR_8_1	e3g3bE1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_1	ECOD (1.6)
C	LRR_8_1	e3g3bC1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_1	ECOD (1.6)
A	LRR_8_1	e3g3bA1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
F	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
D	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)
E	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
C	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
A	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF00062	C-type lysozyme/alpha-lactalbumin family (Lys)	C-type lysozyme/alpha-lactalbumin family	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bac ...	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bacterial cell walls. Structure is a multi-domain, mixed alpha and beta fold, containing four conserved disulfide bonds.	Domain
A, C, E, G	PF13855	Leucine rich repeat (LRR_8)	Leucine rich repeat	-	Repeat
A, C, E, G	PF01462	Leucine rich repeat N-terminal domain (LRRNT)	Leucine rich repeat N-terminal domain	-	Family
A, C, E, G	PF11921	Domain of unknown function (DUF3439) (DUF3439)	Domain of unknown function (DUF3439)	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Lysozyme C	hydrolase activity, acting on glycosyl bonds hexosaminidase activity beta-N-acetylhexosaminidase activity beta-N-acetylglucosaminidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity peptidoglycan muralytic activity lysozyme activity identical protein binding protein binding binding	catabolic process cell wall organization or biogenesis metabolic process cellular process macromolecule metabolic process macromolecule catabolic process cell wall macromolecule catabolic process cell wall macromolecule metabolic process biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing response to stimulus catabolic process cell wall organization or biogenesis metabolic process cellular process macromolecule metabolic process macromolecule catabolic process cell wall macromolecule catabolic process cell wall macromolecule metabolic process biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing response to stimulus response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium response to bacterium response to stress response to external biotic stimulus defense response to Gram-positive bacterium	cellular anatomical structure intracellular anatomical structure cytoplasm extracellular region extracellular space membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system
A, C, E, G	variable lymphocyte receptor VLRB.2D	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR001916	Glycoside hydrolase, family 22	Family
B, D, F, H	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
B, D, F, H	IPR019799	Glycoside hydrolase family 22 domain	Domain
B, D, F, H	IPR000974	Glycoside hydrolase, family 22, lysozyme	Family
A, C, E, G	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, C, E, G	IPR000372	Leucine-rich repeat N-terminal domain	Domain
A, C, E, G	IPR024592	Variable lymphocyte receptor, C-terminal	Domain
A, C, E, G	IPR001611	Leucine-rich repeat	Repeat
A, C, E, G	IPR003591	Leucine-rich repeat, typical subtype	Repeat

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.