3KH2

Crystal structure of the P1 bacteriophage Doc toxin (F68S) in complex with the Phd antitoxin (L17M/V39A). Northeast Structural Genomics targets ER385-ER386

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)
E	SCOP2B Superfamily	YefM-like	8092244	3000907	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YefM-like	8092244	3000907	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	YefM-like	8092244	3000907	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	YefM-like	8092244	3000907	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	PF02661	e3kh2A1	A: alpha bundles	X: Fic-like (From Topology)	H: Fic-like (From Topology)	T: Fic-like	F: PF02661	ECOD (1.6)
B	PF02661	e3kh2B1	A: alpha bundles	X: Fic-like (From Topology)	H: Fic-like (From Topology)	T: Fic-like	F: PF02661	ECOD (1.6)
C	PF02661	e3kh2C1	A: alpha bundles	X: Fic-like (From Topology)	H: Fic-like (From Topology)	T: Fic-like	F: PF02661	ECOD (1.6)
D	PF02661	e3kh2D1	A: alpha bundles	X: Fic-like (From Topology)	H: Fic-like (From Topology)	T: Fic-like	F: PF02661	ECOD (1.6)
E	PF02604	e3kh2E1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PF02604	ECOD (1.6)
F	PF02604	e3kh2F1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PF02604	ECOD (1.6)
G	PF02604	e3kh2G1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PF02604	ECOD (1.6)
H	PF02604	e3kh2H1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PF02604	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.1870	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Fic/DOC protein, Fido domain	CATH (4.3.0)
B	1.20.120.1870	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Fic/DOC protein, Fido domain	CATH (4.3.0)
C	1.20.120.1870	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Fic/DOC protein, Fido domain	CATH (4.3.0)
D	1.20.120.1870	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Fic/DOC protein, Fido domain	CATH (4.3.0)
E	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
F	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
G	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
H	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02661	Fic/DOC family (Fic)	Fic/DOC family	-	Family
E, F, G, H	PF02604	Antitoxin Phd_YefM, type II toxin-antitoxin system (PhdYeFM_antitox)	Antitoxin Phd_YefM, type II toxin-antitoxin system	Members of this family act as antitoxins in type II toxin-antitoxin systems [1]. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin [2] ...	Members of this family act as antitoxins in type II toxin-antitoxin systems [1]. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin [2]. This domain complexes with Txe toxins containing Pfam:PF06769, Fic/DOC toxins containing Pfam:PF02661 and YafO toxins containing Pfam:PF13957.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Death on curing protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine kinase activity	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process biological process involved in interspecies interaction between organisms killing by virus of host cell by post-segregational killing disruption of cell in another organism disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing biological process involved in interaction with host phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process biological process involved in interspecies interaction between organisms killing by virus of host cell by post-segregational killing disruption of cell in another organism disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host translation symbiont-mediated suppression of host gene expression modulation by symbiont of host process symbiont-mediated suppression of host translation symbiont-mediated perturbation of host gene expression modulation of process of another organism	-
E, F, G, H	Prevent host death protein	DNA binding binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity sequence-specific DNA binding molecular sequestering activity toxin sequestering activity transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process	protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006440	Death on curing protein	Family
A, B, C, D	IPR003812	Fido domain	Domain
E, F, G, H	IPR006442	Type II toxin-antitoxin system, antitoxin Phd/YefM	Family
E, F, G, H	IPR036165	YefM-like superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.