4QPO | pdb_00004qpo

Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4qpod_	All alpha proteins	IHF-like DNA-binding proteins	IHF-like DNA-binding proteins	DNA-binding domain (fragment?) of the TraM protein	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d4qpoc_	All alpha proteins	IHF-like DNA-binding proteins	IHF-like DNA-binding proteins	DNA-binding domain (fragment?) of the TraM protein	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4qpob_	All alpha proteins	IHF-like DNA-binding proteins	IHF-like DNA-binding proteins	DNA-binding domain (fragment?) of the TraM protein	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4qpoa_	All alpha proteins	IHF-like DNA-binding proteins	IHF-like DNA-binding proteins	DNA-binding domain (fragment?) of the TraM protein	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	IHF-like DNA-binding proteins	8073273	3000426	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	IHF-like DNA-binding proteins	8073273	3000426	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	IHF-like DNA-binding proteins	8073273	3000426	SCOP2B (2022-06-29)
A	SCOP2 Family	DNA-binding domain (fragment?) of the TraM protein	8073272	4003039	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	IHF-like DNA-binding proteins	8073273	3000426	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	Tra_M_N	e4qpoD1	A: alpha arrays	X: HTH	H: DNA-binding domain of TraM protein (From Topology)	T: DNA-binding domain of TraM protein	F: Tra_M_N	ECOD (1.6)
C	Tra_M_N	e4qpoC1	A: alpha arrays	X: HTH	H: DNA-binding domain of TraM protein (From Topology)	T: DNA-binding domain of TraM protein	F: Tra_M_N	ECOD (1.6)
B	Tra_M_N	e4qpoB1	A: alpha arrays	X: HTH	H: DNA-binding domain of TraM protein (From Topology)	T: DNA-binding domain of TraM protein	F: Tra_M_N	ECOD (1.6)
A	Tra_M_N	e4qpoA1	A: alpha arrays	X: HTH	H: DNA-binding domain of TraM protein (From Topology)	T: DNA-binding domain of TraM protein	F: Tra_M_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.2.0)
C	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.2.0)
B	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.2.0)
A	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05261	TraM protein, DNA-binding (Tra_M)	TraM protein, DNA-binding	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Relaxosome protein TraM	DNA binding binding nucleic acid binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR010992	Integration host factor (IHF)-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR042073	TraM, DNA-binding domain	Homologous Superfamily
A, B, C, D	IPR007925	Relaxosome protein TraM	Family

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.