4QPQ | pdb_00004qpq

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

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)
H	SCOP2B Superfamily	IHF-like DNA-binding proteins	8073273	3000426	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	IHF-like DNA-binding proteins	8073273	3000426	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	IHF-like DNA-binding proteins	8073273	3000426	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	IHF-like DNA-binding proteins	8073273	3000426	SCOP2B (2022-06-29)
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	SCOP2B Superfamily	IHF-like DNA-binding proteins	8073273	3000426	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)
H	Tra_M_N	e4qpqH1	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)
G	Tra_M_N	e4qpqG1	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)
F	Tra_M_N	e4qpqF1	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)
E	Tra_M_N	e4qpqE1	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)
D	Tra_M_N	e4qpqD1	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	e4qpqC1	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	e4qpqB1	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	e4qpqA1	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)
H	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.3.0)
G	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.3.0)
F	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.3.0)
E	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.3.0)
D	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.3.0)
C	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.3.0)
B	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.3.0)
A	1.10.10.450	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	TraM protein, DNA-binding	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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
J [auth Q]	sbmA DNA2	-	-	-
I [auth P]	sbmA DNA1	-	-	-
A, B, C, D, E A, B, C, D, E, F, G, H	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, E A, B, C, D, E, F, G, H	IPR010992	Integration host factor (IHF)-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR042073	TraM, DNA-binding domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	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.