2IT0 | pdb_00002it0

Crystal structure of a two-domain IdeR-DNA complex crystal form II

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
F [auth D]	d2it0d1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
F [auth D]	d2it0d2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent regulator	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
E [auth C]	d2it0c1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
E [auth C]	d2it0c2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent regulator	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D [auth B]	d2it0b1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D [auth B]	d2it0b2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent regulator	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D [auth B]	d2it0b3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C [auth A]	d2it0a1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C [auth A]	d2it0a2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent regulator	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C [auth A]	d2it0a3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth D]	Phage_CII	e2it0D1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (develop294)
F [auth D]	P53_tetramer	e2it0D2	A: alpha bundles	X: EGF-like	H: p53 tetramerization domain	T: p53 tetramerization domain	F: P53_tetramer	ECOD (develop294)
E [auth C]	Phage_CII	e2it0C1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (develop294)
E [auth C]	P53_tetramer	e2it0C2	A: alpha bundles	X: EGF-like	H: p53 tetramerization domain	T: p53 tetramerization domain	F: P53_tetramer	ECOD (develop294)
D [auth B]	Phage_CII	e2it0B1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (develop294)
D [auth B]	P53_tetramer	e2it0B2	A: alpha bundles	X: EGF-like	H: p53 tetramerization domain	T: p53 tetramerization domain	F: P53_tetramer	ECOD (develop294)
C [auth A]	Phage_CII	e2it0A1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (develop294)
C [auth A]	P53_tetramer	e2it0A2	A: alpha bundles	X: EGF-like	H: p53 tetramerization domain	T: p53 tetramerization domain	F: P53_tetramer	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
F [auth D]	1.10.60.10	Mainly Alpha	Orthogonal Bundle	Diphtheria Toxin Repressor	domain 2	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)
E [auth C]	1.10.60.10	Mainly Alpha	Orthogonal Bundle	Diphtheria Toxin Repressor	domain 2	CATH (4.3.0)
D [auth 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)
C [auth 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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], D [auth B], E [auth C], F [auth D]	Iron-dependent repressor ideR	serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity peptidoglycan L,D-transpeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity carboxypeptidase activity acyltransferase activity transferase activity	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan-protein cross-linking peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis macromolecule metabolic process cell wall macromolecule metabolic process cellular component organization cell wall organization external encapsulating structure organization	cellular anatomical structure extracellular region
B [auth F]	mbtA/mbtB operator strand 2	-	-	-
A [auth E]	mbtA/mbtB operator strand 1	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B], E [auth C], F [auth D]	IPR050979	Bacterial L,D-transpeptidase	Family
C [auth A], D [auth B], E [auth C], F [auth D]	IPR041280	Bacterial Ig domain, transpeptidase-associated	Domain
C [auth A], D [auth B], E [auth C], F [auth D]	IPR005490	L,D-transpeptidase catalytic domain	Domain
C [auth A], D [auth B], E [auth C], F [auth D]	IPR038063	L,D-transpeptidase catalytic domain-like	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.