5UP9 | pdb_00005up9

Crystal Structure of Zn-bound Human Heavy-Chain ferritin variant 122H-delta C-star with para-xylenedihydroxamate

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)
F	d5up9f_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	(Apo)ferritin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5up9e_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	(Apo)ferritin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5up9d_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	(Apo)ferritin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5up9c_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	(Apo)ferritin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5up9b_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	(Apo)ferritin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5up9a_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	(Apo)ferritin	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)
F	SCOP2B Superfamily	Ferritin-like	8038756	3001658	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ferritin-like	8038756	3001658	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ferritin-like	8038756	3001658	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ferritin-like	8038756	3001658	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ferritin-like	8038756	3001658	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ferritin-like	8038756	3001658	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)
F	Utp12	e5up9F1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Utp12	ECOD (develop294)
E	Utp12	e5up9E1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Utp12	ECOD (develop294)
D	Utp12	e5up9D1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Utp12	ECOD (develop294)
C	Utp12	e5up9C1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Utp12	ECOD (develop294)
B	Utp12	e5up9B1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Utp12	ECOD (develop294)
A	Utp12	e5up9A1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Utp12	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
E	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
D	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
C	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
B	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
A	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00210	Ferritin-like domain (Ferritin)	Ferritin-like domain	This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Ferritin heavy chain	molecular sequestering activity iron ion sequestering activity metal ion sequestering activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding ferric iron binding oxidoreductase activity, acting on metal ions oxidoreductase activity molecular sequestering activity iron ion sequestering activity metal ion sequestering activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding ferric iron binding oxidoreductase activity, acting on metal ions oxidoreductase activity ferroxidase activity oxidoreductase activity, acting on metal ions, oxygen as acceptor catalytic activity identical protein binding protein 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 localization transport iron ion transport transition metal ion transport 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 localization transport iron ion transport transition metal ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport response to stimulus immune response immune system process negative regulation of ferroptosis regulation of biological process regulation of cellular process negative regulation of programmed cell death biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of cellular process cellular process regulation of ferroptosis ferroptosis programmed cell death negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation fibroblast proliferation regulation of fibroblast proliferation negative regulation of fibroblast proliferation	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle vacuole autophagosome tertiary granule lumen tertiary granule autolysosome lytic vacuole secondary lysosome lysosome ferritin complex protein-containing complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR009040	Ferritin-like diiron domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR012347	Ferritin-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR009078	Ferritin-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR008331	Ferritin/DPS domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001519	Ferritin	Family
A, B, C, D, E A, B, C, D, E, F	IPR014034	Ferritin, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: P02794	hemochromatosis type 5 malignant glioma malignant mesothelioma melancholia contact dermatitis Iron Overload mixed glioma keloid endogenous depression neurodegenerative disease non-small cell lung carcinoma asthma precancerous condition subependymal giant cell astrocytoma glioma hemochromatosis type 5 malignant glioma malignant mesothelioma melancholia contact dermatitis Iron Overload mixed glioma keloid endogenous depression neurodegenerative disease non-small cell lung carcinoma asthma precancerous condition subependymal giant cell astrocytoma glioma lung cancer ovarian cancer atypical teratoid rhabdoid tumor ulcerative colitis dermatomyositis lymphoplasmacytic lymphoma medulloblastoma neurotic disorder plasma cell myeloma psoriasis depressive disorder hepatocellular carcinoma large cell medulloblastoma

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.