5VXJ | pdb_00005vxj

2.50 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-E3

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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)
J	d5vxjj_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
H	d5vxjh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
F	d5vxjf_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
D	d5vxjd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
B	d5vxjb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
I	d5vxji_	All alpha proteins	IpaD-like	IpaD-like	IpaD-like	automated matches	(Shigella flexneri ) [TaxId: 623 ],	SCOPe (2.08)
G	d5vxjg_	All alpha proteins	IpaD-like	IpaD-like	IpaD-like	automated matches	(Shigella flexneri ) [TaxId: 623 ],	SCOPe (2.08)
E	d5vxje_	All alpha proteins	IpaD-like	IpaD-like	IpaD-like	automated matches	(Shigella flexneri ) [TaxId: 623 ],	SCOPe (2.08)
C	d5vxjc_	All alpha proteins	IpaD-like	IpaD-like	IpaD-like	automated matches	(Shigella flexneri ) [TaxId: 623 ],	SCOPe (2.08)
A	d5vxja_	All alpha proteins	IpaD-like	IpaD-like	IpaD-like	automated matches	(Shigella flexneri ) [TaxId: 623 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I	SCOP2B Superfamily	IpaD-like	8042947	3001578	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	IpaD-like	8042947	3001578	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	IpaD-like	8042947	3001578	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	IpaD-like	8042947	3001578	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	IpaD-like	8042947	3001578	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)
J	V-set_8	e5vxjJ1	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)
H	V-set_8	e5vxjH1	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	V-set_8	e5vxjF1	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	V-set_8	e5vxjD1	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)
B	V-set_8	e5vxjB1	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)
I	IpaD	e5vxjI1	A: alpha bundles	X: IpaD-like (From Topology)	H: IpaD-like (From Topology)	T: IpaD-like	F: IpaD	ECOD (1.6)
G	IpaD	e5vxjG1	A: alpha bundles	X: IpaD-like (From Topology)	H: IpaD-like (From Topology)	T: IpaD-like	F: IpaD	ECOD (1.6)
E	IpaD	e5vxjE1	A: alpha bundles	X: IpaD-like (From Topology)	H: IpaD-like (From Topology)	T: IpaD-like	F: IpaD	ECOD (1.6)
C	IpaD	e5vxjC1	A: alpha bundles	X: IpaD-like (From Topology)	H: IpaD-like (From Topology)	T: IpaD-like	F: IpaD	ECOD (1.6)
A	IpaD	e5vxjA1	A: alpha bundles	X: IpaD-like (From Topology)	H: IpaD-like (From Topology)	T: IpaD-like	F: IpaD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I	1.20.1710.10	Mainly Alpha	Up-down Bundle	IpaD-like	IpaD-like	CATH (4.3.0)
G	1.20.1710.10	Mainly Alpha	Up-down Bundle	IpaD-like	IpaD-like	CATH (4.3.0)
E	1.20.1710.10	Mainly Alpha	Up-down Bundle	IpaD-like	IpaD-like	CATH (4.3.0)
C	1.20.1710.10	Mainly Alpha	Up-down Bundle	IpaD-like	IpaD-like	CATH (4.3.0)
A	1.20.1710.10	Mainly Alpha	Up-down Bundle	IpaD-like	IpaD-like	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
B, D, F, H, J	VH JMK-E3	VH	Vicugna pacos (alpaca)	IGHV3S5301, IGHJ401	V-DOMAIN VH	IG	VH	IMGT (202549-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D, F, H, J	Heavy Chain	IGHV1	-	invasin ipad	SAbDab (2025-12-19)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J	single-domain antibody JMK-E3	-	-	-
A, C, E, G, I	Invasin IpaD	-	symbiont-mediated perturbation of host cellular process effector-mediated perturbation of host defenses by symbiont biological process involved in interspecies interaction between organisms symbiont-mediated activation of host programmed cell death response to stimulus response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated perturbation of host process symbiont-mediated suppression of host innate immune response effector-mediated perturbation of host process by symbiont symbiont-mediated perturbation of host innate immune response effector-mediated activation of host programmed cell death by symbiont response to host symbiont-mediated perturbation of host cellular process effector-mediated perturbation of host defenses by symbiont biological process involved in interspecies interaction between organisms symbiont-mediated activation of host programmed cell death response to stimulus response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated perturbation of host process symbiont-mediated suppression of host innate immune response effector-mediated perturbation of host process by symbiont symbiont-mediated perturbation of host innate immune response effector-mediated activation of host programmed cell death by symbiont response to host response to external biotic stimulus modulation of process of another organism symbiont-mediated perturbation of host defense response response to other organism symbiont-mediated perturbation of host programmed cell death symbiont-mediated perturbation of host immune response effector-mediated suppression of host innate immune response symbiont-mediated response to host defenses response to external stimulus biological process involved in interaction with host effector-mediated perturbation of host innate immune response by symbiont effector-mediated suppression of host defense response	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I	IPR009483	Type III secretion systems tip complex component IpaD/BipD/SipD	Family
A, C, E, G, I	IPR036708	BipD-like 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.