3CKD | pdb_00003ckd

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)
C	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)
A	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)
C		e3ckdC1	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: RNA_pol_Rpb2_2	F:	ECOD (20:10:01)
B		e3ckdB2	A: Glutamine synthetase-like	X: Glutamine synthetase/guanido kinase	H: Glutamine synthetase/guanido kinase	T: Cu_amine_oxid	F:	ECOD (20:10:01)
A		e3ckdA1	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)

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	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process symbiont-mediated perturbation of host cellular process effector-mediated perturbation of host defenses by symbiont biological process involved in interspecies interaction between organisms catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process 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 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 suppression of host programmed cell death	cellular anatomical structure extracellular region host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR051071	Leucine-rich repeat-containing bacterial E3 ubiquitin ligases	Family
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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.