3CKD

Crystal structure of the C-terminal domain of the Shigella type III effector IpaH

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	Novel E3 ligase (NEL) C-terminal domain -like	8052845	3002145	SCOP2B (2022-06-29)
B	SCOP2 Family	Novel E3 ligase (NEL) C-terminal domain-like	8050055	4006749	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Novel E3 ligase (NEL) C-terminal domain -like	8052845	3002145	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Novel E3 ligase (NEL) C-terminal domain -like	8052845	3002145	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	PF14496	e3ckdA1	A: alpha arrays	X: Novel E3 ligase (NEL) (From Topology)	H: Novel E3 ligase (NEL) (From Topology)	T: Novel E3 ligase (NEL)	F: PF14496	ECOD (1.6)
B	PF14496	e3ckdB2	A: alpha arrays	X: Novel E3 ligase (NEL) (From Topology)	H: Novel E3 ligase (NEL) (From Topology)	T: Novel E3 ligase (NEL)	F: PF14496	ECOD (1.6)
C	PF14496	e3ckdC1	A: alpha arrays	X: Novel E3 ligase (NEL) (From Topology)	H: Novel E3 ligase (NEL) (From Topology)	T: Novel E3 ligase (NEL)	F: PF14496	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1270.130	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
A	1.20.58.360	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	1.20.58.90	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	1.20.1270.130	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
B	1.20.58.360	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	1.20.58.90	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
C	1.20.1270.130	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
C	1.20.58.360	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
C	1.20.58.90	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF14496	C-terminal novel E3 ligase, LRR-interacting (NEL)	C-terminal novel E3 ligase, LRR-interacting	This NEL or novel E3 ligase domain is found at the C-terminus of bacterial virulence factors. Its sequence is different from those of the eukaryotic HECT and RING-finger E3 ligases, and it subverts the host ubiquitination process. At the N-terminus o ...	This NEL or novel E3 ligase domain is found at the C-terminus of bacterial virulence factors. Its sequence is different from those of the eukaryotic HECT and RING-finger E3 ligases, and it subverts the host ubiquitination process. At the N-terminus of the family-members there is a series of LRR repeats, and the NEL domain interacts with the most N-terminal repeat. The key residue for the ligation step is the cysteine, eg found at position 386 in UniProtKB:E7K2H2. The LRR section sequesters this active site until invasion has occurred [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal 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 symbiont-mediated suppression of host programmed cell death	extracellular region cellular anatomical entity host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B, C	IPR001611	Leucine-rich repeat	Repeat
A, B, C	IPR032674	LRR-containing bacterial E3 ligase, N-terminal	Domain
A, B, C	IPR029487	Novel E3 ligase domain	Domain

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.