3KXE | pdb_00003kxe

A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex

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)
D	SCOP2B Superfamily	Ribbon-helix-helix	8052310	3000295	SCOP2B (2022-06-29)
C	SCOP2 Family	ParD antitoxin-like	8044732	4004105	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Ribbon-helix-helix	8052310	3000295	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	ParD_antitoxin	e3kxeD2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: ParD_antitoxin	ECOD (v294.1)
D	Peptidase_M24	e3kxeD3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Peptidase_M24	ECOD (v294.1)
C	CBS	e3kxeC1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (v294.1)
B	RVP	e3kxeB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
A	eIF-1a	e3kxeA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: HTH	T: winged helix domain	F: eIF-1a	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	6.10.10.120	Special	Helix non-globular	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	6.10.10.120	Special	Helix non-globular	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
A	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05016	ParE toxin of type II toxin-antitoxin system, parDE (ParE_toxin)	ParE toxin of type II toxin-antitoxin system, parDE	ParE is the toxin family of a type II toxin-antitoxin family. It is toxic towards DNA gyrase, but is neutralised by the antitoxin ParD. The family also encompasses RelE/ParE described in [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Antitoxin protein parD-1	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	protein-containing complex organization protein heterotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein heterooligomerization regulation of cellular process RNA metabolic process regulation of primary metabolic process protein-containing complex organization protein heterotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein heterooligomerization regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	-
A, B	Toxin protein parE-1	-	protein-containing complex organization protein heterotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein heterooligomerization	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR022789	Antitoxin ParD	Family
C, D	IPR038296	Antitoxin ParD superfamily	Homologous Superfamily
C, D	IPR010985	Ribbon-helix-helix	Homologous Superfamily
A, B	IPR007712	Toxin-antitoxin system, RelE/ParE toxin family	Family
A, B	IPR051803	Type II TA system RelE-like toxin	Family
A, B	IPR028344	Toxin-antitoxin system, toxin component ParE1/4	Family
A, B	IPR035093	Toxin-antitoxin system, RelE/ParE toxin domain 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.