1L5J | pdb_00001l5j

CRYSTAL STRUCTURE OF E. COLI ACONITASE B.

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)
B	d1l5jb1	All alpha proteins	alpha-alpha superhelix	Aconitase B, N-terminal domain	Aconitase B, N-terminal domain	Aconitase B, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1l5jb2	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	LeuD-like	Aconitase B, second N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1l5jb3	Alpha and beta proteins (a/b)	Aconitase iron-sulfur domain	Aconitase iron-sulfur domain	Aconitase iron-sulfur domain	Aconitase B, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1l5ja1	All alpha proteins	alpha-alpha superhelix	Aconitase B, N-terminal domain	Aconitase B, N-terminal domain	Aconitase B, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1l5ja2	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	LeuD-like	Aconitase B, second N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1l5ja3	Alpha and beta proteins (a/b)	Aconitase iron-sulfur domain	Aconitase iron-sulfur domain	Aconitase iron-sulfur domain	Aconitase B, C-terminal domain	(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)
B	SCOP2B Superfamily	LeuD/IlvD-like	8041087	3000947	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aconitase iron-sulfur domain	8041089	3001516	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aconitase B, N-terminal domain	8041083	3000650	SCOP2B (2022-06-29)
A	SCOP2 Family	Aconitase B, N-terminal domain	8028704	4001990	SCOP2 (2022-06-29)
A	SCOP2 Family	LeuD-like	8028708	4003492	SCOP2 (2022-06-29)
A	SCOP2 Family	Aconitase iron-sulfur domain	8028710	4000810	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aconitase B, N-terminal domain	8041083	3000650	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LeuD/IlvD-like	8041087	3000947	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aconitase iron-sulfur domain	8041089	3001516	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		e1l5jB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F:	ECOD (v294.1)
B	Glyco_hydro_20b	e1l5jB3	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Glyco_hydro_20b	ECOD (v294.1)
B	Aconitase	e1l5jB4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Aconitase	ECOD (v294.1)
B		e1l5jB6	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F:	ECOD (v294.1)
A	Aconitase_B_N	e1l5jA1	A: alpha bundles	X: Repetitive alpha hairpins	H: ARM repeat	T: ARM repeat	F: Aconitase_B_N	ECOD (v294.1)
A	Aconitase_C	e1l5jA3	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain	T: The swivelling beta/beta/alpha domain	F: Aconitase_C	ECOD (v294.1)
A	PALP	e1l5jA5	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: PriB N-terminal domain-like	T: PriB N-terminal domain-like	F: PALP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.25.40.310	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Aconitate B, HEAT-like domain	CATH (4.3.0)
B	3.20.19.10	Alpha Beta	Alpha-Beta Barrel	Aconitase	domain 4	CATH (4.3.0)
B	3.40.1060.10	Alpha Beta	3-Layer(aba) Sandwich	Aconitase	Domain 2	CATH (4.3.0)
B	3.30.499.10	Alpha Beta	2-Layer Sandwich	Aconitase	domain 3	CATH (4.3.0)
A	1.25.40.310	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Aconitate B, HEAT-like domain	CATH (4.3.0)
A	3.20.19.10	Alpha Beta	Alpha-Beta Barrel	Aconitase	domain 4	CATH (4.3.0)
A	3.40.1060.10	Alpha Beta	3-Layer(aba) Sandwich	Aconitase	Domain 2	CATH (4.3.0)
A	3.30.499.10	Alpha Beta	2-Layer Sandwich	Aconitase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF11791	Aconitate B N-terminal domain (Aconitase_B_N)	Aconitate B N-terminal domain	-	Repeat
A, B	PF00330	Aconitase family (aconitate hydratase) (Aconitase)	Aconitase family (aconitate hydratase)	-	Family
A, B	PF06434	Aconitate hydratase 2 N-terminus (Aconitase_2_N)	Aconitate hydratase 2 N-terminus	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Aconitate hydratase 2	RNA binding binding nucleic acid binding mRNA binding aconitate hydratase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity 2-methylisocitrate dehydratase activity mRNA 3'-UTR binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding RNA binding binding nucleic acid binding mRNA binding aconitate hydratase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity 2-methylisocitrate dehydratase activity mRNA 3'-UTR binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aldehyde metabolic process small molecule metabolic process monocarboxylic acid metabolic process regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process macromolecule metabolic process protein metabolic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004406	Aconitase B	Family
A, B	IPR015929	Aconitase B, swivel	Domain
A, B	IPR050926	Aconitase/IPM Isomerase	Family
A, B	IPR036288	Aconitase B, HEAT-like domain superfamily	Homologous Superfamily
A, B	IPR015932	Aconitase, domain 2	Homologous Superfamily
A, B	IPR036008	Aconitase, iron-sulfur domain	Homologous Superfamily
A, B	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain	Domain
A, B	IPR015928	Aconitase/3-isopropylmalate dehydratase, swivel	Homologous Superfamily
A, B	IPR015931	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3	Homologous Superfamily
A, B	IPR015933	Aconitase B, HEAT-like domain	Domain
A, B	IPR018136	Aconitase family, 4Fe-4S cluster binding site	Binding Site

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.