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
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)
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)
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)
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)
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)
E	SCOP2B Superfamily	Immunoglobulin-binding domains-like	8085561	3000399	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)
G	SAG	e1yntG1	A: beta sandwiches	X: Cupredoxin-like	H: Surface antigen 1 (SAG1)-related-sequence (SRS) family (From Topology)	T: Surface antigen 1 (SAG1)-related-sequence (SRS) family	F: SAG	ECOD (1.6)
F	SAG	e1yntF1	A: beta sandwiches	X: Cupredoxin-like	H: Surface antigen 1 (SAG1)-related-sequence (SRS) family (From Topology)	T: Surface antigen 1 (SAG1)-related-sequence (SRS) family	F: SAG	ECOD (1.6)
E	B1	e1yntE1	A: a+b two layers	X: beta-Grasp	H: Immunoglobulin-binding domains (From Topology)	T: Immunoglobulin-binding domains	F: B1	ECOD (1.6)
D	V-set_8	e1yntD2	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)
D	C1-set_1	e1yntD1	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)
B	V-set_8	e1yntB2	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	C1-set_1	e1yntB1	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)
C	C1-set_4	e1yntC2	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)
C	V-set	e1yntC1	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)
A	C1-set_4	e1yntA2	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	V-set	e1yntA1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
E	3.10.20.10	Alpha Beta	Roll	Ubiquitin-like (UB roll)		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 (202546-0)
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 (202546-0)

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 (2025-11-28)
A, C	Light Chain	IGKV10	Kappa	major surface antigen p30 \| protein l, major surface antigen p30	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F, G	PF04092	SRS domain (SAG)	SRS domain	-	Family
E	PF02246	Protein L b1 domain (B1)	Protein L b1 domain	Protein L is a bacterial protein with immunoglobulin (Ig) light chain-binding properties. It contains a number of homologous b1 repeats towards the N-terminus. These repeats have been found to be responsible for the interaction of protein L with Ig l ...	Protein L is a bacterial protein with immunoglobulin (Ig) light chain-binding properties. It contains a number of homologous b1 repeats towards the N-terminus. These repeats have been found to be responsible for the interaction of protein L with Ig light chains [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, G	Major surface antigen p30	-	-	cellular anatomical structure membrane symbiont-containing vacuole
E	protein L	protein-containing complex binding binding immunoglobulin binding IgG binding	-	cellular anatomical structure extracellular region
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
F, G	IPR036755	SRS domain superfamily	Homologous Superfamily
F, G	IPR028352	Protozoan surface antigen, SAG1 family	Family
F, G	IPR007226	SRS domain	Domain
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 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.