5VXJ

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
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	d5vxja_	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)
E	d5vxje_	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)
I	d5vxji_	All alpha proteins	IpaD-like	IpaD-like	IpaD-like	automated matches	(Shigella flexneri ) [TaxId: 623 ],	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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	IpaD-like	8042947	3001578	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	IpaD-like	8042947	3001578	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	IpaD-like	8042947	3001578	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	IpaD-like	8042947	3001578	SCOP2B (2022-06-29)
I	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)
A	PF06511	e5vxjA1	A: alpha bundles	X: IpaD-like (From Topology)	H: IpaD-like (From Topology)	T: IpaD-like	F: PF06511	ECOD (1.6)
C	PF06511	e5vxjC1	A: alpha bundles	X: IpaD-like (From Topology)	H: IpaD-like (From Topology)	T: IpaD-like	F: PF06511	ECOD (1.6)
E	PF06511	e5vxjE1	A: alpha bundles	X: IpaD-like (From Topology)	H: IpaD-like (From Topology)	T: IpaD-like	F: PF06511	ECOD (1.6)
G	PF06511	e5vxjG1	A: alpha bundles	X: IpaD-like (From Topology)	H: IpaD-like (From Topology)	T: IpaD-like	F: PF06511	ECOD (1.6)
I	PF06511	e5vxjI1	A: alpha bundles	X: IpaD-like (From Topology)	H: IpaD-like (From Topology)	T: IpaD-like	F: PF06511	ECOD (1.6)
B	PF07686	e5vxjB1	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	e5vxjD1	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)
F	PF07686	e5vxjF1	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)
H	PF07686	e5vxjH1	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)
J	PF07686	e5vxjJ1	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	1.20.1710.10	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)
E	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)
I	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 (202418-0)

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 (2024-05-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I	PF06511	Type III secretion systems tip complex components (T3SS_TC)	Type III secretion systems tip complex components	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

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 R01GM133198.