4ZM2 | pdb_00004zm2

Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat in a monoclinic space group

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	YefM-like	8092244	3000907	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YefM-like	8092244	3000907	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YefM-like	8092244	3000907	SCOP2B (2022-06-29)
A	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)
D	Transthyretin	e4zm2D1	A: a/b three-layered sandwiches	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: Transthyretin	ECOD (v294.1)
C	Transthyretin	e4zm2C1	A: a/b three-layered sandwiches	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: Transthyretin	ECOD (v294.1)
B	Transthyretin	e4zm2B1	A: a/b three-layered sandwiches	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: Transthyretin	ECOD (v294.1)
A	Transthyretin	e4zm2A1	A: a/b three-layered sandwiches	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: Transthyretin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
C	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
B	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
A	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	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
F, H	DNA (5'-D(CPAPTPGPTPGPTPAPCPAPCPAPAP*G)-3')	-	-	-
E, G	DNA (5'-D(GPCPTPTPGPTPGPTPAPCPAPCPAP*T)-3')	-	-	-
A, B, C, D	Antitoxin phd	DNA binding 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 RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process	protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006442	Type II toxin-antitoxin system, antitoxin Phd/YefM	Family
A, B, C, D	IPR036165	YefM-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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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