3OPZ

Crystal structure of trans-sialidase in complex with the Fab fragment of a neutralizing monoclonal IgG antibody

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8037009	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sialidases	8037008	3001607	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sialidases	8037008	3001607	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8037009	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8037009	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sialidases	8037008	3001607	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	Laminin_G_3	e3opzB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Laminin_G_3	ECOD (1.6)
B	BNR_2	e3opzB2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: BNR_2	ECOD (1.6)
C	Laminin_G_3	e3opzC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Laminin_G_3	ECOD (1.6)
C	BNR_2	e3opzC2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: BNR_2	ECOD (1.6)
A	Laminin_G_3	e3opzA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Laminin_G_3	ECOD (1.6)
A	BNR_2	e3opzA2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: BNR_2	ECOD (1.6)
D [auth H]	V-set_8	e3opzH1	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 [auth H]	C1-set_1	e3opzH2	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)
F [auth J]	V-set_8	e3opzJ1	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)
F [auth J]	C1-set_1	e3opzJ2	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 I]	V-set_8	e3opzI1	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 I]	C1-set_1	e3opzI2	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)
H [auth M]	C1-set_4	e3opzM2	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)
H [auth M]	V-set	e3opzM1	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)
I [auth N]	C1-set_4	e3opzN2	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)
I [auth N]	V-set	e3opzN1	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)
G [auth L]	C1-set_4	e3opzL2	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)
G [auth L]	V-set	e3opzL1	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)
B	2.120.10.10	Mainly Beta	6 Propeller	Neuraminidase		CATH (4.3.0)
B	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.120.10.10	Mainly Beta	6 Propeller	Neuraminidase		CATH (4.3.0)
C	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
A	2.120.10.10	Mainly Beta	6 Propeller	Neuraminidase		CATH (4.3.0)
A	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth J]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth N]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth L]	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
D [auth H], E [auth I], F [auth J]	Fab fragment of immunoglobulin G	VH-CH1	Mus musculus (house mouse)	IGHV1-6302, IGHJ201, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202443-0)
G [auth L], H [auth M], I [auth N]	Fab fragment of immunoglobulin G	L-KAPPA	Mus musculus (house mouse)	IGKV4-8001, IGKJ203, IGKJ401, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202443-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth H], E [auth I], F [auth J]	Heavy Chain	IGHV1	-	trans-sialidase	SAbDab (2024-11-01)
G [auth L], H [auth M], I [auth N]	Light Chain	IGKV4	Kappa	trans-sialidase	SAbDab (2024-11-01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF13859	BNR repeat-like domain (BNR_3)	BNR repeat-like domain	-	Repeat
A, B, C	PF22925	Trans-sialidase, C-terminal domain (TS_C)	Trans-sialidase, C-terminal domain	This domain is found C-terminal in a number of Trans-sialidases (TS) from Trypanosoma cruzi and other related species. The Trypanosoma TS is involved in host cell invasion and parasite survival in the bloodstream. The parasite uses TS activity to sia ...	This domain is found C-terminal in a number of Trans-sialidases (TS) from Trypanosoma cruzi and other related species. The Trypanosoma TS is involved in host cell invasion and parasite survival in the bloodstream. The parasite uses TS activity to sialylate its own surface molecules, allowing it to evade lysis by serum factors. This domain follows the catalytic domain and adopts a beta-sandwich fold typical for Concanavalin-like lectin/glucanase superfamily. It is likely involved in binding glycan structures present on the surface of the Trypanosomes or host cells and in modulating the activity and biological function of TS [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Trans-sialidase	hydrolase activity, acting on glycosyl bonds alpha-sialidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity exo-alpha-sialidase activity catalytic activity	sphingolipid catabolic process ganglioside catabolic process catabolic process glycolipid metabolic process carbohydrate derivative metabolic process cellular lipid catabolic process cellular catabolic process ceramide catabolic process amide metabolic process membrane lipid metabolic process ceramide metabolic process carbohydrate derivative catabolic process glycosphingolipid catabolic process lipid catabolic process sphingolipid catabolic process ganglioside catabolic process catabolic process glycolipid metabolic process carbohydrate derivative metabolic process cellular lipid catabolic process cellular catabolic process ceramide catabolic process amide metabolic process membrane lipid metabolic process ceramide metabolic process carbohydrate derivative catabolic process glycosphingolipid catabolic process lipid catabolic process glycosphingolipid metabolic process cellular metabolic process liposaccharide metabolic process primary metabolic process sphingolipid metabolic process membrane lipid catabolic process glycolipid catabolic process cellular lipid metabolic process metabolic process cellular process ganglioside metabolic process lipid metabolic process carbohydrate metabolic process oligosaccharide catabolic process oligosaccharide metabolic process carbohydrate catabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cellular anatomical entity membrane cytoplasm
D [auth H], E [auth I], F [auth J]	heavy chain of the Fab fragment of immunoglobulin G	-	-	-
G [auth L], H [auth M], I [auth N]	light chain of the Fab fragment of immunoglobulin G	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B, C	IPR011040	Sialidase	Domain
A, B, C	IPR026856	Sialidase family	Family
A, B, C	IPR008377	Trypanosome sialidase	Family
A, B, C	IPR036278	Sialidase 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.