6DBG

Crystal Structure of VHH R303 in complex with InlB-LRR-IR

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	d6dbga2	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
A	d6dbga1	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)
B	d6dbgb2	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
B	d6dbgb1	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)
C	d6dbgc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Camelus dromedarius ) [TaxId: 9838 ],	SCOPe (2.08)
D	d6dbgd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Camelus dromedarius ) [TaxId: 9838 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	L domain-like	8036334	3001010	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	E set domains	8055069	3000070	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	E set domains	8055069	3000070	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L domain-like	8036334	3001010	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	LRR_adjacent	e6dbgA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LRR_adjacent	ECOD (1.6)
A	LRR_9	e6dbgA3	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	e6dbgA2	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: Internalin_N	ECOD (1.6)
B	LRR_adjacent	e6dbgB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LRR_adjacent	ECOD (1.6)
B	LRR_9	e6dbgB1	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)
B	Internalin_N	e6dbgB3	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: Internalin_N	ECOD (1.6)
C	V-set_12	e6dbgC1	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)
D	V-set_12	e6dbgD1	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)

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 (4.3.0)
B	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, D	Heavy Chain	IGHV1	-	internalin b	SAbDab (2024-12-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF12354	Bacterial adhesion/invasion protein N terminal (Internalin_N)	Bacterial adhesion/invasion protein N terminal	This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00560, Pfam:PF08191, Pfam:PF09479. There are two completely conserved residues (I and F) that may be functionally i ...	This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00560, Pfam:PF08191, Pfam:PF09479. There are two completely conserved residues (I and F) that may be functionally important. Internalin mediates bacterial adhesion and invasion of epithelial cells in the human intestine through specific interaction with its host cell receptor E-cadherin. This family is the N terminal of internalin, the cap domain of the protein. The cap domain is conserved between different internalin types. The cap domain does not interact with E cadherin, therefore its function is presumably structural: capping the hydrophobic core.	Domain
A, B	PF12799	Leucine Rich repeats (2 copies) (LRR_4)	Leucine Rich repeats (2 copies)	-	Repeat
A, B	PF08191	LRR adjacent (LRR_adjacent)	LRR adjacent	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Internalin B	binding lipid binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	-	cellular anatomical structure extracellular region cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm
C, D	VHH R303	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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