8DFG | pdb_00008dfg

Crystal structure of potently neutralizing human monoclonal antibody 42D6 Fab in complex with MSP1-19

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth A]	EGF_3	e8dfgA1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: EGF_3	ECOD (1.6)
F [auth A]	EGF_MSP1_1	e8dfgA2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: EGF_MSP1_1	ECOD (1.6)
E [auth B]	EGF_3	e8dfgB2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: EGF_3	ECOD (1.6)
E [auth B]	EGF_MSP1_1	e8dfgB1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: EGF_MSP1_1	ECOD (1.6)
D [auth M]	C1-set_4	e8dfgM2	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 M]	V-set	e8dfgM1	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)
B [auth L]	C1-set_4	e8dfgL1	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)
B [auth L]	V-set	e8dfgL2	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 I]	V-set_8	e8dfgI2	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)
C [auth I]	C1-set_1	e8dfgI1	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 H]	V-set_8	e8dfgH1	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)
A [auth H]	C1-set_1	e8dfgH2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L], D [auth M]	Light Chain	IGKV3	Kappa	merozoite surface protein 1	SAbDab (2025-12-19)
A [auth H], C [auth I]	Heavy Chain	IGHV4	-	merozoite surface protein 1	SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth B], F [auth A]	PF12946	MSP1 EGF domain 1 (EGF_MSP1_1)	MSP1 EGF domain 1	This EGF-like domain is found at the C-terminus of the malaria parasite MSP1 protein. MSP1 is the merozoite surface protein 1. This domain is part of the C-terminal fragment that is proteolytically processed from the the rest of the protein and is le ...	This EGF-like domain is found at the C-terminus of the malaria parasite MSP1 protein. MSP1 is the merozoite surface protein 1. This domain is part of the C-terminal fragment that is proteolytically processed from the the rest of the protein and is left attached to the surface of the invading parasite.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth B], F [auth A]	Merozoite surface protein 1	-	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle entry into host cell by a symbiont-containing vacuole biological process involved in interaction with host biological process involved in symbiotic interaction	cellular anatomical structure membrane side of membrane cell periphery plasma membrane vacuolar membrane membrane-bounded organelle intracellular anatomical structure vacuole intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle cytoplasm cellular anatomical structure membrane side of membrane cell periphery plasma membrane vacuolar membrane membrane-bounded organelle intracellular anatomical structure vacuole intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle cytoplasm organelle membrane extracellular region
B [auth L], D [auth M]	42D6 Fab Light Chain	-	-	-
A [auth H], C [auth I]	42D6 Fab Heavy Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth B], F [auth A]	IPR010901	Merozoite surface 1, C-terminal	Domain
E [auth B], F [auth A]	IPR024730	Merozoite surface protein, EGF domain 1	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.