5F3J

Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT 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)
A	SCOP2B Superfamily	Duffy binding domain-like	8078551	3001914	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Duffy binding domain-like	8078551	3001914	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)
A	PF05424	e5f3jA1	A: alpha bundles	X: Duffy-binding-like domain, N-terminal subdomain (From Topology)	H: Duffy-binding-like domain, N-terminal subdomain (From Topology)	T: Duffy-binding-like domain, N-terminal subdomain	F: PF05424	ECOD (1.6)
A	PF03011	e5f3jA2	A: alpha bundles	X: Duffy-binding-like domain, C-terminal subdomain (From Topology)	H: Duffy-binding-like domain, C-terminal subdomain (From Topology)	T: Duffy-binding-like domain, C-terminal subdomain	F: PF03011	ECOD (1.6)
B	PF05424	e5f3jB1	A: alpha bundles	X: Duffy-binding-like domain, N-terminal subdomain (From Topology)	H: Duffy-binding-like domain, N-terminal subdomain (From Topology)	T: Duffy-binding-like domain, N-terminal subdomain	F: PF05424	ECOD (1.6)
B	PF03011	e5f3jB2	A: alpha bundles	X: Duffy-binding-like domain, C-terminal subdomain (From Topology)	H: Duffy-binding-like domain, C-terminal subdomain (From Topology)	T: Duffy-binding-like domain, C-terminal subdomain	F: PF03011	ECOD (1.6)
C	PF07686	e5f3jC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D	PF07686	e5f3jD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1310.20	Mainly Alpha	Up-down Bundle	5 helical Cullin repeat like	Duffy-antigen binding domain	CATH (4.3.0)
A	1.20.58.830	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	1.20.1310.20	Mainly Alpha	Up-down Bundle	5 helical Cullin repeat like	Duffy-antigen binding domain	CATH (4.3.0)
B	1.20.58.830	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	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
C, D	2D10	SCFV-KAPPA-HEAVY	Mus musculus (house mouse)	IGKV2-11201, IGKJ501, IGHV1-8201, IGHJ201	V-DOMAIN V-KAPPA, V-DOMAIN VH	IG	SCFV-KAPPA-HEAVY	IMGT (202416-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05424	Duffy binding domain (Duffy_binding)	Duffy binding domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Duffy receptor	identical protein binding protein binding binding host cell surface binding host cell surface receptor binding	-	membrane cellular anatomical entity
C, D	Antibody 2D10 single chain variable fragment	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR043057	Erythrocyte binding antigen 175, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR008602	Duffy-antigen binding domain	Domain
A, B	IPR021620	Erythrocyte binding antigen 175, C-terminal	Domain
A, B	IPR021015	Duffy-antigen binding, C-terminal	Domain
A, B	IPR042202	Duffy-antigen binding superfamily	Homologous Superfamily
A, B	IPR021032	Duffy-antigen binding, N-terminal	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.