2P5L | pdb_00002p5l

Crystal structure of a dimer of N-terminal domains of AhrC in complex with an 18bp DNA operator site

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)
H	d2p5lh1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
G	d2p5lg1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F [auth D]	d2p5ld1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E [auth C]	d2p5lc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Winged helix DNA-binding domain	8058558	3000034	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Winged helix DNA-binding domain	8058558	3000034	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Winged helix DNA-binding domain	8058558	3000034	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Winged helix DNA-binding domain	8058558	3000034	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	Pox_D5	e2p5lH1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pox_D5	ECOD (v294.1)
G	Pox_D5	e2p5lG1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pox_D5	ECOD (v294.1)
F [auth D]	Pox_D5	e2p5lD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pox_D5	ECOD (v294.1)
E [auth C]	Pox_D5	e2p5lC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pox_D5	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
G	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
F [auth D]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
E [auth C]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth C], F [auth D], G, H	PF01316	Arginine repressor, DNA binding domain (Arg_repressor)	Arginine repressor, DNA binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth C], F [auth D], G, H	Arginine repressor	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity cation binding organic acid binding ion binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity cation binding organic acid binding ion binding anion binding amino acid binding carboxylic acid binding arginine binding small molecule binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis L-arginine biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis L-arginine biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process L-amino acid biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process arginine metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process small molecule metabolic process alpha-amino acid biosynthetic process regulation of cellular process regulation of arginine biosynthetic process regulation of amino acid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process regulation of amino acid metabolic process regulation of biosynthetic process regulation of biological process biological regulation regulation of metabolic process	protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm
B, D [auth F]	DNA (5'-D(DCPDTPDTPDGPDAPDAPDTPDTPDTPDTPDTPDAPDTPDTPDCPDAPDTPDG)-3')	-	-	-
A, C [auth E]	DNA (5'-D(DCPDAPDTPDGPDAPDAPDTPDAPDAPDAPDAPDAPDTPDTPDCPDAPDAPDG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth C], F [auth D], G, H	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
E [auth C], F [auth D], G, H	IPR001669	Arginine repressor	Family
E [auth C], F [auth D], G, H	IPR020899	Arginine repressor, C-terminal	Domain
E [auth C], F [auth D], G, H	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
E [auth C], F [auth D], G, H	IPR020900	Arginine repressor, DNA-binding domain	Domain
E [auth C], F [auth D], G, H	IPR036251	Arginine repressor, C-terminal 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.