1IXC | pdb_00001ixc

Crystal structure of CbnR, a LysR family transcriptional regulator

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d1ixcb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	LysR-like transcriptional regulators	LysR-type regulatory protein CbnR	(Cupriavidus necator ) [TaxId: 106590 ],	SCOPe (2.08)
B	d1ixcb2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	LysR-type regulatory protein CbnR	(Cupriavidus necator ) [TaxId: 106590 ],	SCOPe (2.08)
A	d1ixca1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	LysR-like transcriptional regulators	LysR-type regulatory protein CbnR	(Cupriavidus necator ) [TaxId: 106590 ],	SCOPe (2.08)
A	d1ixca2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	LysR-type regulatory protein CbnR	(Cupriavidus necator ) [TaxId: 106590 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8017746	3000083	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8017744	3000034	SCOP2B (2022-06-29)
A	SCOP2 Family	LysR-like transcriptional regulators	8002826	4000316	SCOP2 (2022-06-29)
A	SCOP2 Family	Phosphate binding protein-like	8002827	4000229	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8017744	3000034	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Type 2 solute binding protein-like	8017746	3000083	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)
B		e1ixcB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Fe_dep_repress	F:	ECOD (20:10:01)
B		e1ixcB2	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: LysR_substrate	F:	ECOD (20:10:01)
A		e1ixcA1	A: HTH	X: HTH	H: winged helix domain	T: HTH_1	F:	ECOD (20:10:01)
A		e1ixcA3	A: Alpha-beta plaits	X: Protease propeptides/inhibitors	H: Protease propeptides/inhibitors	T: LysR_substrate	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
A	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)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	LysR-type regulatory protein	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity	-	protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR005119	LysR, substrate-binding	Domain
A, B	IPR000847	LysR, HTH, N-terminal domain	Domain
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR036390	Winged helix DNA-binding 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.