1D5Y | pdb_00001d5y

CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA

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)
E [auth A]	d1d5ya1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	AraC type transcriptional activator	Rob transcription factor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth A]	d1d5ya3	Alpha and beta proteins (a+b)	Probable bacterial effector-binding domain	Probable bacterial effector-binding domain	Rob transcription factor, C-terminal domain	Rob transcription factor, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth A]	d1d5ya4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth D]	d1d5yd1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	AraC type transcriptional activator	Rob transcription factor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth D]	d1d5yd3	Alpha and beta proteins (a+b)	Probable bacterial effector-binding domain	Probable bacterial effector-binding domain	Rob transcription factor, C-terminal domain	Rob transcription factor, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth D]	d1d5yd4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G [auth C]	d1d5yc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	AraC type transcriptional activator	Rob transcription factor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G [auth C]	d1d5yc3	Alpha and beta proteins (a+b)	Probable bacterial effector-binding domain	Probable bacterial effector-binding domain	Rob transcription factor, C-terminal domain	Rob transcription factor, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G [auth C]	d1d5yc4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H [auth B]	d1d5yb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	AraC type transcriptional activator	Rob transcription factor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H [auth B]	d1d5yb3	Alpha and beta proteins (a+b)	Probable bacterial effector-binding domain	Probable bacterial effector-binding domain	Rob transcription factor, C-terminal domain	Rob transcription factor, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H [auth B]	d1d5yb4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2 Family	AraC type transcriptional activator	8002467	4000332	SCOP2 (2022-06-29)
E [auth A]	SCOP2 Family	Rob transcription factor, C-terminal domain	8002468	4000297	SCOP2 (2022-06-29)
E [auth A]	SCOP2 Superfamily	Homeodomain-like	8091564	3000001	SCOP2 (2022-06-29)
E [auth A]	SCOP2 Superfamily	Probable bacterial effector-binding domain	8002469	3000062	SCOP2 (2022-06-29)
E [auth A]	SCOP2 Superfamily	Homeodomain-like	8091563	3000001	SCOP2 (2022-06-29)
F [auth D]	SCOP2B Superfamily	Homeodomain-like	8091563	3000001	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Probable bacterial effector-binding domain	8002469	3000062	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Homeodomain-like	8091564	3000001	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	Homeodomain-like	8091563	3000001	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	Homeodomain-like	8091564	3000001	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	Probable bacterial effector-binding domain	8002469	3000062	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	Homeodomain-like	8091564	3000001	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	Probable bacterial effector-binding domain	8002469	3000062	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	Homeodomain-like	8091563	3000001	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)
E [auth A]	HTH_AraC_2	e1d5yA4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HTH_AraC_2	ECOD (1.6)
E [auth A]	HTH_18_1	e1d5yA2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HTH_18_1	ECOD (1.6)
E [auth A]	GyrI-like	e1d5yA3	A: a+b duplicates or obligate multimers	X: Probable bacterial effector-binding domain (From Topology)	H: Probable bacterial effector-binding domain (From Topology)	T: Probable bacterial effector-binding domain	F: GyrI-like	ECOD (1.6)
F [auth D]	HTH_AraC_2	e1d5yD4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HTH_AraC_2	ECOD (1.6)
F [auth D]	HTH_18_1	e1d5yD2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HTH_18_1	ECOD (1.6)
F [auth D]	GyrI-like	e1d5yD3	A: a+b duplicates or obligate multimers	X: Probable bacterial effector-binding domain (From Topology)	H: Probable bacterial effector-binding domain (From Topology)	T: Probable bacterial effector-binding domain	F: GyrI-like	ECOD (1.6)
G [auth C]	HTH_AraC_2	e1d5yC4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HTH_AraC_2	ECOD (1.6)
G [auth C]	HTH_18_1	e1d5yC2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HTH_18_1	ECOD (1.6)
G [auth C]	GyrI-like	e1d5yC3	A: a+b duplicates or obligate multimers	X: Probable bacterial effector-binding domain (From Topology)	H: Probable bacterial effector-binding domain (From Topology)	T: Probable bacterial effector-binding domain	F: GyrI-like	ECOD (1.6)
H [auth B]	HTH_AraC_2	e1d5yB4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HTH_AraC_2	ECOD (1.6)
H [auth B]	HTH_18_1	e1d5yB2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HTH_18_1	ECOD (1.6)
H [auth B]	GyrI-like	e1d5yB3	A: a+b duplicates or obligate multimers	X: Probable bacterial effector-binding domain (From Topology)	H: Probable bacterial effector-binding domain (From Topology)	T: Probable bacterial effector-binding domain	F: GyrI-like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth A]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
E [auth A]	3.20.80.10	Alpha Beta	Alpha-Beta Barrel	Multidrug-efflux Transporter 1 Regulator Bmrr	Chain A	CATH (4.3.0)
F [auth D]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
F [auth D]	3.20.80.10	Alpha Beta	Alpha-Beta Barrel	Multidrug-efflux Transporter 1 Regulator Bmrr	Chain A	CATH (4.3.0)
G [auth C]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
G [auth C]	3.20.80.10	Alpha Beta	Alpha-Beta Barrel	Multidrug-efflux Transporter 1 Regulator Bmrr	Chain A	CATH (4.3.0)
H [auth B]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
H [auth B]	3.20.80.10	Alpha Beta	Alpha-Beta Barrel	Multidrug-efflux Transporter 1 Regulator Bmrr	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth D], G [auth C], H [auth B]	PF06445	GyrI-like small molecule binding domain (GyrI-like)	GyrI-like small molecule binding domain	This family contains the small molecule binding domain of a number of different bacterial transcription activators [1]. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecu ...	This family contains the small molecule binding domain of a number of different bacterial transcription activators [1]. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding [3]. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira [3].	Domain
E [auth A], F [auth D], G [auth C], H [auth B]	PF12833	Helix-turn-helix domain (HTH_18)	Helix-turn-helix domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth N], D [auth P]	DNA (5'-D(APCPTPTPTPGPAPCPAPTPTPCPAPGPTPGPCPTPGPTP*C)-3')	-	-	-
E [auth A], F [auth D], G [auth C], H [auth B]	ROB TRANSCRIPTION FACTOR	basal transcription machinery binding protein binding binding bacterial-type RNA polymerase holo enzyme binding transcription regulator activity DNA-binding transcription factor activity sequence-specific DNA binding DNA binding nucleic acid binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological 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 cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
A [auth M], C [auth O]	DNA (5'-D(TPGPAPCPAPGPCPAPCPTPGPAPAPTPGPTPCPAPAPAP*G)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth D], G [auth C], H [auth B]	IPR009057	Homedomain-like superfamily	Homologous Superfamily
E [auth A], F [auth D], G [auth C], H [auth B]	IPR018060	AraC-like, DNA binding HTH domain	Domain
E [auth A], F [auth D], G [auth C], H [auth B]	IPR018062	HTH domain AraC-type, conserved site	Conserved Site
E [auth A], F [auth D], G [auth C], H [auth B]	IPR011256	Regulatory factor, effector binding domain superfamily	Homologous Superfamily
E [auth A], F [auth D], G [auth C], H [auth B]	IPR020449	Transcription regulator HTH, AraC- type, HTH domain	Domain
E [auth A], F [auth D], G [auth C], H [auth B]	IPR010499	Bacterial transcription activator, effector binding	Domain
E [auth A], F [auth D], G [auth C], H [auth B]	IPR050959	Multiple antibiotic resistance protein MarA-like	Family
E [auth A], F [auth D], G [auth C], H [auth B]	IPR029442	GyrI-like small molecule binding domain	Domain

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.