6DBF | pdb_00006dbf

Crystal Structure of VHH R303 in complex with InlB-LRR

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d6dbfb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Camelus dromedarius ) [TaxId: 9838 ],	SCOPe (2.08)
A	d6dbfa_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	Internalin LRR domain	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	V-set_12	e6dbfB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
A	LRR_9	e6dbfA1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_9	ECOD (1.6)
A	Internalin_N	e6dbfA2	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: Internalin_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV1	-	listeria virulence factor inlb	SAbDab (2026-01-16)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	InlB specific VHH R303	-	-	-
A	Listeria virulence factor InlB	binding lipid binding cation binding ion binding metal ion binding small molecule binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	biological process involved in interspecies interaction between organisms entry of bacterium into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction	cellular anatomical structure extracellular region cell surface cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR025875	Leucine rich repeat 4	Repeat
A	IPR025987	GW domain	Domain
A	IPR013378	Internalin B-like, B-repeat	Repeat
A	IPR001611	Leucine-rich repeat	Repeat
A	IPR038200	GW domain superfamily	Homologous Superfamily
A	IPR012569	Internalin, Ig-like inter-repeat region	Domain
A	IPR024634	Internalin, N-terminal	Domain
A	IPR042229	Listeria-Bacteroides repeat domain superfamily	Homologous Superfamily
A	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A	IPR014755	Copper resistance protein CopC/internalin, immunoglobulin-like	Homologous Superfamily
A	IPR050836	SDS22/Internalin LRR-containing	Family

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.