1FBI

CRYSTAL STRUCTURE OF A CROSS-REACTION COMPLEX BETWEEN FAB F9.13.7 AND GUINEA-FOWL LYSOZYME

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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 [auth H]	d1fbih1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d1fbih2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d1fbih3	Artifacts	Tags	Tags	Tags	N-terminal Tags	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth Q]	d1fbiq1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth Q]	d1fbiq2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth Q]	d1fbiq3	Artifacts	Tags	Tags	Tags	N-terminal Tags	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d1fbil1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d1fbil2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth P]	d1fbip1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth P]	d1fbip2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth X]	d1fbix_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	Lysozyme	helmeted guineafowl (Numida meleagris ) [TaxId: 8996 ],	SCOPe (2.08)
F [auth Y]	d1fbiy_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	Lysozyme	helmeted guineafowl (Numida meleagris ) [TaxId: 8996 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth L]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091539	3000071	SCOP2B (2022-06-29)
D [auth P]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091539	3000071	SCOP2B (2022-06-29)
C [auth X]	SCOP2B Superfamily	Lysozyme-like	8033686	3001879	SCOP2B (2022-06-29)
F [auth Y]	SCOP2B Superfamily	Lysozyme-like	8033686	3001879	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 [auth H]	V-set_8	e1fbiH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B [auth H]	C1-set_1	e1fbiH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
E [auth Q]	V-set_8	e1fbiQ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E [auth Q]	C1-set_1	e1fbiQ2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
A [auth L]	C1-set_4	e1fbiL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
A [auth L]	V-set	e1fbiL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
D [auth P]	C1-set_4	e1fbiP2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth P]	V-set	e1fbiP1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
C [auth X]	Lys	e1fbiX1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)
F [auth Y]	Lys	e1fbiY1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth Q]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth P]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth X]	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
F [auth Y]	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B [auth H], E [auth Q]	F9.13.7, anti-lysozyme [hen egg white]	VH-CH1	Mus musculus (house mouse)	IGHV1-6902, IGHJ202, IGHJ203, IGHG101	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202446-0)
A [auth L], D [auth P]	F9.13.7, anti-lysozyme [hen egg white]	L-KAPPA	Mus musculus (house mouse)	IGKV10-9601, IGKV10-9602, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202446-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H], E [auth Q]	Heavy Chain	IGHV1	-	guinea fowl lysozyme	SAbDab (2024-11-15)
A [auth L], D [auth P]	Light Chain	IGKV10	Kappa	guinea fowl lysozyme	SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth H], E [auth Q]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
A [auth L], D [auth P]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
C [auth X], F [auth Y]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth H], E [auth Q]	IGG1 F9.13.7 FAB (HEAVY CHAIN)	protein binding binding signaling receptor binding immunoglobulin receptor binding antigen binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process membrane organization import into cell transport establishment of localization vesicle-mediated transport cellular component organization localization phagocytosis, engulfment membrane invagination cellular process phagocytosis cellular component organization or biogenesis endocytosis plasma membrane invagination positive regulation of acute inflammatory response to antigenic stimulus regulation of immune effector process regulation of acute inflammatory response to antigenic stimulus positive regulation of leukocyte mediated immunity inflammatory response to antigenic stimulus positive regulation of hypersensitivity positive regulation of inflammatory response positive regulation of adaptive immune response positive regulation of immunoglobulin mediated immune response hypersensitivity regulation of adaptive immune response response to external stimulus regulation of inflammatory response regulation of B cell mediated immunity regulation of leukocyte mediated immunity positive regulation of defense response regulation of acute inflammatory response inflammatory response positive regulation of type I hypersensitivity regulation of type I hypersensitivity regulation of defense response regulation of response to external stimulus positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of acute inflammatory response positive regulation of B cell mediated immunity type I hypersensitivity positive regulation of response to external stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains response to stress regulation of response to stress regulation of immunoglobulin mediated immune response positive regulation of immune effector process acute inflammatory response regulation of hypersensitivity defense response regulation of inflammatory response to antigenic stimulus acute inflammatory response to antigenic stimulus positive regulation of inflammatory response to antigenic stimulus regulation of lymphocyte mediated immunity myeloid leukocyte mediated immunity antibody-dependent cellular cytotoxicity leukocyte mediated cytotoxicity type II hypersensitivity type IIa hypersensitivity cell killing developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation anatomical structure development leukocyte differentiation regulation of myeloid leukocyte mediated immunity regulation of type IIa hypersensitivity regulation of type II hypersensitivity positive regulation of myeloid leukocyte mediated immunity positive regulation of type IIa hypersensitivity positive regulation of type II hypersensitivity humoral immune response complement activation humoral immune response mediated by circulating immunoglobulin complement activation, classical pathway activation of immune response biological process involved in interspecies interaction between organisms response to other organism antibacterial humoral response defense response to symbiont antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to bacterium response to external biotic stimulus regulation of localization positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization positive regulation of endocytosis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis positive regulation of transport phagocytosis, recognition cell recognition	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein-containing complex extracellular region extracellular space immunoglobulin complex, circulating immunoglobulin complex intracellular anatomical structure cytoplasm
A [auth L], D [auth P]	IGG1 F9.13.7 FAB (LIGHT CHAIN)	-	developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development cellular process leukocyte differentiation	cell periphery cellular anatomical structure plasma membrane membrane extracellular region
C [auth X], F [auth Y]	GUINEA FOWL LYSOZYME	hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus cellular process disruption of cell in another organism disruption of anatomical structure in another organism biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus cellular process 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
B [auth H], E [auth Q]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth H], E [auth Q]	IPR050380	Immune Recognition and Response Modulators	Family
B [auth H], E [auth Q]	IPR003597	Immunoglobulin C1-set	Domain
B [auth H], E [auth Q]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth H], E [auth Q]	IPR007110	Immunoglobulin-like domain	Domain
A [auth L], D [auth P]	IPR003597	Immunoglobulin C1-set	Domain
A [auth L], D [auth P]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth L], D [auth P]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth L], D [auth P]	IPR007110	Immunoglobulin-like domain	Domain
A [auth L], D [auth P]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
A [auth L], D [auth P]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C [auth X], F [auth Y]	IPR001916	Glycoside hydrolase, family 22	Family
C [auth X], F [auth Y]	IPR019799	Glycoside hydrolase family 22 domain	Domain
C [auth X], F [auth Y]	IPR000974	Glycoside hydrolase, family 22, lysozyme	Family
C [auth X], F [auth Y]	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.