4DYU | pdb_00004dyu

The crystal structure of DNA starvation/stationary phase protection protein Dps from Yersinia pestis KIM 10

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)
L	d4dyul_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)
K	d4dyuk_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)
J	d4dyuj_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)
I	d4dyui_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)
H	d4dyuh_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)
G	d4dyug_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)
F	d4dyuf_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)
E	d4dyue_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)
D	d4dyud_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)
C	d4dyuc_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)
B	d4dyub_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)
A	d4dyua_	All alpha proteins	Ferritin-like	Ferritin-like	Ferritin	automated matches	(Yersinia pestis KIM10+ ) [TaxId: 187410 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	Ferritin-like	8075802	3001658	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ferritin-like	8075802	3001658	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ferritin-like	8075802	3001658	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ferritin-like	8075802	3001658	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ferritin-like	8075802	3001658	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ferritin-like	8075802	3001658	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ferritin-like	8075802	3001658	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ferritin-like	8075802	3001658	SCOP2B (2022-06-29)
D	SCOP2 Family	Ferritin	8075801	4000839	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Ferritin-like	8075802	3001658	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Ferritin-like	8075802	3001658	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ferritin-like	8075802	3001658	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ferritin-like	8075802	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)
L	Fer4_13	e4dyuL2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)
K	Fer4_13	e4dyuK2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)
J	Fer4_13	e4dyuJ2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)
I	Fer4_13	e4dyuI2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)
H	Fer4_13	e4dyuH2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)
G	Fer4_13	e4dyuG2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)
F	Fer4_13	e4dyuF2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)
E	Fer4_13	e4dyuE2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)
D	Fer4_13	e4dyuD2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)
C	Fer4_13	e4dyuC2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)
B	Fer4_13	e4dyuB2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)
A	Fer4_13	e4dyuA2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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, G, H, I, J, K, L	DNA protection during starvation protein	DNA binding binding nucleic acid binding oxidoreductase activity, acting on metal ions oxidoreductase activity catalytic activity cation binding ferric iron binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule 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 regulation of DNA-templated DNA replication initiation regulation of cellular process negative regulation of biological process negative regulation of DNA-templated DNA replication initiation 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 regulation of DNA-templated DNA replication initiation regulation of cellular process negative regulation of biological process negative regulation of DNA-templated DNA replication initiation regulation of primary metabolic process nucleobase-containing compound metabolic process negative regulation of DNA-templated DNA replication negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process DNA-templated DNA replication regulation of biological process negative regulation of DNA replication DNA replication initiation negative regulation of metabolic process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process DNA replication regulation of DNA-templated DNA replication metabolic process cellular process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process cellular component organization organelle organization chromosome condensation chromosome organization cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure DnaA-Dps complex protein-DNA complex intracellular membraneless organelle chromosome replication inhibiting complex intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome cytoplasm

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	IPR002177	DNA-binding protein Dps	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR012347	Ferritin-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR009078	Ferritin-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR023067	DNA protection during starvation protein, gammaproteobacteria	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR008331	Ferritin/DPS domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR023188	DNA-binding protein Dps, conserved site	Conserved 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.