2B3Y | pdb_00002b3y

Structure of a monoclinic crystal form of human cytosolic aconitase (IRP1)

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2b3yb1	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	LeuD-like	ron-responsive element binding protein 1, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2b3yb2	Alpha and beta proteins (a/b)	Aconitase iron-sulfur domain	Aconitase iron-sulfur domain	Aconitase iron-sulfur domain	Iron-responsive element binding protein 1, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2b3ya1	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	LeuD-like	ron-responsive element binding protein 1, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2b3ya2	Alpha and beta proteins (a/b)	Aconitase iron-sulfur domain	Aconitase iron-sulfur domain	Aconitase iron-sulfur domain	Iron-responsive element binding protein 1, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	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	8037595	3000947	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aconitase iron-sulfur domain	8037597	3001516	SCOP2B (2022-06-29)
A	SCOP2 Family	LeuD-like	8025216	4003492	SCOP2 (2022-06-29)
A	SCOP2 Family	Aconitase iron-sulfur domain	8025218	4000810	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LeuD/IlvD-like	8037595	3000947	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aconitase iron-sulfur domain	8037597	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)
A		e2b3yA3	A: Aconitase iron-sulfur domain	X: Aconitase iron-sulfur domain	H: Aconitase iron-sulfur domain II	T: Aconitase	F:	ECOD (20:10:01)
A		e2b3yA1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: PepX_N	F:	ECOD (20:10:01)
A		e2b3yA2	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: SRP54_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.499.10	Alpha Beta	2-Layer Sandwich	Aconitase	domain 3	CATH (4.3.0)
B	3.40.1060.10	Alpha Beta	3-Layer(aba) Sandwich	Aconitase	Domain 2	CATH (4.3.0)
B	6.10.190.10	Special	Helix non-globular	Apolipoprotein Cii	Chain: A	CATH (4.3.0)
B	3.20.19.10	Alpha Beta	Alpha-Beta Barrel	Aconitase	domain 4	CATH (4.3.0)
A	3.30.499.10	Alpha Beta	2-Layer Sandwich	Aconitase	domain 3	CATH (4.3.0)
A	3.40.1060.10	Alpha Beta	3-Layer(aba) Sandwich	Aconitase	Domain 2	CATH (4.3.0)
A	6.10.190.10	Special	Helix non-globular	Apolipoprotein Cii	Chain: A	CATH (4.3.0)
A	3.20.19.10	Alpha Beta	Alpha-Beta Barrel	Aconitase	domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00330	Aconitase family (aconitate hydratase) (Aconitase)	Aconitase family (aconitate hydratase)	-	Family
A, B	PF00694	Aconitase C-terminal domain (Aconitase_C)	Aconitase C-terminal domain	Members of this family usually also match to Pfam:PF00330. This domain undergoes conformational change in the enzyme mechanism [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Iron-responsive element binding protein 1	iron-sulfur cluster binding binding metal cluster binding small molecule binding aconitate hydratase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity 3 iron, 4 sulfur cluster binding RNA binding iron-responsive element binding nucleic acid binding mRNA binding iron-sulfur cluster binding binding metal cluster binding small molecule binding aconitate hydratase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity 3 iron, 4 sulfur cluster binding RNA binding iron-responsive element binding nucleic acid binding mRNA binding translation regulator activity mRNA regulatory element binding translation repressor activity translation repressor activity 4 iron, 4 sulfur cluster binding cation binding ion binding metal ion binding	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process primary metabolic process generation of precursor metabolites and energy intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process primary metabolic process generation of precursor metabolites and energy nucleotide metabolic process NADP+ metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process NADPH regeneration purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process citrate metabolic process multicellular organismal process system process digestion intestinal absorption digestive system process response to iron(II) ion response to stimulus response to metal ion response to iron ion response to chemical aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds developmental process multicellular organism development anatomical structure development post-embryonic development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol Golgi apparatus endomembrane system endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain	Domain
A, B	IPR044137	Aconitase A, swivel domain	Domain
A, B	IPR018136	Aconitase family, 4Fe-4S cluster binding site	Binding Site
A, B	IPR000573	Aconitase A/isopropylmalate dehydratase small subunit, swivel domain	Domain
A, B	IPR036008	Aconitase, iron-sulfur domain	Homologous Superfamily
A, B	IPR006249	Aconitase/Iron-responsive element-binding protein 2	Family
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P21399	Neoplasm Invasiveness adenoma breast carcinoma invasive ductal breast carcinoma pancreatic ductal adenocarcinoma adrenal cortex carcinoma breast fibroadenoma lung cancer osteoarthritis osteosarcoma breast cancer ductal breast carcinoma in situ malignant mesothelioma osteoarthritis susceptibility 1 ovarian cancer

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.