1YNT | pdb_00001ynt

Structure of the monomeric form of T. gondii SAG1 surface antigen bound to a human Fab

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
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)
E	d1ynte_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Immunoglobulin-binding domains	Immunoglobulin-binding domains	Immunoglobulin light chain-binding domain of protein L	(Finegoldia magna ATCC 29328 ) [TaxId: 334413 ],	SCOPe (2.08)
G	d1yntg1	All beta proteins	Cupredoxin-like	Major surface antigen p30, SAG1	Major surface antigen p30, SAG1	automated matches	(Toxoplasma gondii ) [TaxId: 5811 ],	SCOPe (2.08)
F	d1yntf1	All beta proteins	Cupredoxin-like	Major surface antigen p30, SAG1	Major surface antigen p30, SAG1	automated matches	(Toxoplasma gondii ) [TaxId: 5811 ],	SCOPe (2.08)
D	d1yntd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d1yntd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1yntb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1yntb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d1yntc2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d1yntc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1ynta2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1ynta1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Immunoglobulin-binding domains-like	8085561	3000399	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Major surface antigen p30, sag1	8040893	3000818	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Major surface antigen p30, sag1	8040888	3000818	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Major surface antigen p30, sag1	8040893	3000818	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Major surface antigen p30, sag1	8040888	3000818	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	Polyketide_cyc2	e1yntE1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Polyketide_cyc2	ECOD (v294.1)
G	Sod_Cu	e1yntG1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Sod_Cu	ECOD (v294.1)
F	Sod_Cu	e1yntF1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Sod_Cu	ECOD (v294.1)
D	Copper-bind	e1yntD1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
D	MATH_2	e1yntD2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
B	Copper-bind	e1yntB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
B	EF-hand_6	e1yntB2	A: a/b three-layered sandwiches	X: Globin-like	H: Globin-like	T: Globin-like	F: EF-hand_6	ECOD (v294.1)
C	MATH_2	e1yntC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
A	MATH_2	e1yntA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.10.20.10	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
G	2.60.40.1320	Mainly Beta	Sandwich	Immunoglobulin-like	SRS domain	CATH (4.3.0)
F	2.60.40.1320	Mainly Beta	Sandwich	Immunoglobulin-like	SRS domain	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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, D	Fab 4F11E12	VH-CH1	Mus musculus (house mouse)	IGHV1S13701, IGHJ201, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202611-0)
A, C	Fab 4F11E12	L-KAPPA	Mus musculus (house mouse)	IGKV10-9601, IGKJ102, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D	Heavy Chain	IGHV1	-	major surface antigen p30 \| protein l, major surface antigen p30	SAbDab (2026-03-27)
A, C	Light Chain	IGKV10	Kappa	major surface antigen p30 \| protein l, major surface antigen p30	SAbDab (2026-03-27)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	protein L	protein-containing complex binding binding immunoglobulin binding IgG binding	-	-
F, G	Major surface antigen p30	-	-	cellular anatomical structure membrane symbiont-containing vacuole
B, D	4F11E12 Fab variable heavy chain region	-	-	-
A, C	4F11E12 Fab variable light chain region	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
E	IPR020840	Extracellular matrix-binding protein ebh, GA module	Domain
E	IPR003147	Protein L, Ig light chain-binding	Repeat
E	IPR040912	Repeat of unknown function DUF5633	Repeat
E	IPR002988	Protein G-related albumin-binding (GA) module	Domain
E	IPR035152	GA-like domain	Domain
E	IPR019931	LPXTG cell wall anchor motif	Conserved Site
F, G	IPR036755	SRS domain superfamily	Homologous Superfamily
F, G	IPR028352	Protozoan surface antigen, SAG1 family	Family
F, G	IPR007226	SRS 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.