3DP8 | pdb_00003dp8

Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (nickel butane-1,2,4-tricarboxylate form)

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)
C	d3dp8c_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Nickel-binding periplasmic protein NikA	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3dp8b_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Nickel-binding periplasmic protein NikA	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3dp8a_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Nickel-binding periplasmic protein NikA	(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)
C	SCOP2B Superfamily	Type 2 solute binding protein-like	8035860	3000083	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8035860	3000083	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Type 2 solute binding protein-like	8035860	3000083	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)
C		e3dp8C1	A: HTH	X: HTH	H: winged helix domain	T: Rv3651-like_N	F:	ECOD (20:10:01)
C		e3dp8C2	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: LysR_substrate	F:	ECOD (20:10:01)
B		e3dp8B1	A: HTH	X: HTH	H: winged helix domain	T: Rv3651-like_N	F:	ECOD (20:10:01)
B		e3dp8B2	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: LysR_substrate	F:	ECOD (20:10:01)
A		e3dp8A1	A: HTH	X: HTH	H: winged helix domain	T: Rv3651-like_N	F:	ECOD (20:10:01)
A		e3dp8A2	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: LysR_substrate	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
C	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
A	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00496	Bacterial extracellular solute-binding proteins, family 5 Middle (SBP_bac_5)	Bacterial extracellular solute-binding proteins, family 5 Middle	The borders of this family are based on the PDBSum definitions of the domain edges for Swiss:P06202.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Nickel-binding periplasmic protein	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding peptide transmembrane transporter activity transporter activity transmembrane transporter activity tetrapyrrole binding heme binding metal cluster binding	chemotaxis negative chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion peptide transport localization transport establishment of localization nickel cation transport transition metal ion transport monoatomic ion transport chemotaxis negative chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion peptide transport localization transport establishment of localization nickel cation transport transition metal ion transport monoatomic ion transport monoatomic cation transport metal ion transport import into cell nickel cation transmembrane transport import across plasma membrane monoatomic ion transmembrane transport inorganic cation import across plasma membrane transmembrane transport monoatomic cation transmembrane transport inorganic ion import across plasma membrane nickel cation import across plasma membrane cellular process	cellular anatomical structure membrane ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex periplasmic space outer membrane-bounded periplasmic space cellular anatomical structure membrane ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex periplasmic space outer membrane-bounded periplasmic space cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR011980	Metal-staphylopine-binding protein CntA-like	Family
A, B, C	IPR030678	Peptide/nickel binding protein, MppA-type	Family
A, B, C	IPR023765	Solute-binding protein family 5, conserved site	Conserved Site
A, B, C	IPR000914	Solute-binding protein family 5 domain	Domain
A, B, C	IPR039424	Solute-binding protein family 5	Family

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.