1NF4 | pdb_00001nf4

X-Ray Structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different states (reduced structure)

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)
P	d1nf4p_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
O	d1nf4o_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
N	d1nf4n_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
M	d1nf4m_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
L	d1nf4l_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
K	d1nf4k_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
J	d1nf4j_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
I	d1nf4i_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
H	d1nf4h_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
G	d1nf4g_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
F	d1nf4f_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
E	d1nf4e_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
D	d1nf4d_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
C	d1nf4c_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
B	d1nf4b_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
A	d1nf4a_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	Bacterioferritin (cytochrome b1)	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ferritin-like	8033263	3001658	SCOP2B (2022-06-29)
A	SCOP2 Family	Ferritin	8020883	4000839	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ferritin-like	8033263	3001658	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)
P		e1nf4P1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
O		e1nf4O1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
N		e1nf4N1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
M		e1nf4M1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
L		e1nf4L1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
K		e1nf4K1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
J		e1nf4J1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
I		e1nf4I1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
H		e1nf4H1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
G		e1nf4G1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
F		e1nf4F1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
E		e1nf4E1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
D		e1nf4D1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
C		e1nf4C1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
B		e1nf4B1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
A	Rubrerythrin	e1nf4A1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Rubrerythrin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
O	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
N	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
M	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
L	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
K	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
J	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
I	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
H	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
G	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
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)

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, G, H, I, J, K, L, M, N, O, P	bacterioferritin	cation binding ferric iron binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding tetrapyrrole binding heme binding oxidoreductase activity, acting on metal ions oxidoreductase activity ferroxidase activity oxidoreductase activity, acting on metal ions, oxygen as acceptor cation binding ferric iron binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding tetrapyrrole binding heme binding oxidoreductase activity, acting on metal ions oxidoreductase activity ferroxidase activity oxidoreductase activity, acting on metal ions, oxygen as acceptor catalytic activity	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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR009040	Ferritin-like diiron domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR002024	Bacterioferritin	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR012347	Ferritin-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR009078	Ferritin-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR008331	Ferritin/DPS domain	Domain

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.