5XM5 | pdb_00005xm5

Crystal structure of Zinc binding protein ZinT at 1.49 Angstrom from E. coli

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	d5xm5b_	All beta proteins	Lipocalins	Lipocalins	Hypothetical protein YodA	Hypothetical protein YodA	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d5xm5a_	All beta proteins	Lipocalins	Lipocalins	Hypothetical protein YodA	Hypothetical protein YodA	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Lipocalins	8040519	3001332	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lipocalins	8040519	3001332	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)
B	SBP_bac_8	e5xm5B1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: SBP_bac_8	ECOD (develop294)
A	SBP_bac_8	e5xm5A1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: SBP_bac_8	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
A	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09223	ZinT (YodA) periplasmic lipocalin-like zinc-recruitment (ZinT)	ZinT (YodA) periplasmic lipocalin-like zinc-recruitment	ZinT plays a critical role in recruiting periplasmic zinc to the bacterial zinc-uptake complex ZnuABC, consisting of families Pfam:PF01297,Pfam:PF00950, Pfam:PF00005, regulated by the transcription-regulator FUR, Pfam:PF01475 [2,3]. ZinT acts as a Zn ...	ZinT plays a critical role in recruiting periplasmic zinc to the bacterial zinc-uptake complex ZnuABC, consisting of families Pfam:PF01297,Pfam:PF00950, Pfam:PF00005, regulated by the transcription-regulator FUR, Pfam:PF01475 [2,3]. ZinT acts as a Zn2+-buffering protein that delivers Zn2+ to ZnuA (TroA), Pfam:PF01297 [4]. Members of this family of prokaryotic domains were first identified as part of the response of bacteria to a challenge with the toxic heavy metal cadmium. They are able to bind to cadmium, and ensure its subsequent elimination [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Metal-binding protein ZinT	cation binding transition metal ion binding ion binding binding cadmium ion binding metal ion binding small molecule binding zinc ion binding	cellular response to stimulus response to stimulus cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress response to stress response to chemical cellular response to stimulus response to stimulus cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress response to stress response to chemical cellular process response to nutrient levels response to zinc ion starvation cellular response to starvation response to metal ion starvation cellular response to nutrient levels response to starvation cellular response to zinc ion starvation cellular response to metal ion response to metal ion cellular response to cadmium ion response to cadmium ion inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis intracellular zinc ion homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015304	ZinT domain	Domain
A, B	IPR012674	Calycin	Homologous Superfamily

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.