4OFO

Crystal structure of YntA from Yersinia pestis, unliganded form

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	SBP_bac_5_1st	e4ofoD1	A: a+b two layers	X: Alpha-beta plaits	H: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)	T: Oligo-peptide binding protein (OPPA) insertion domain	F: SBP_bac_5_1st	ECOD (1.6)
D	SBP_bac_5_3rd	e4ofoD2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_5_3rd	ECOD (1.6)
D	SBP_bac_5_2nd	e4ofoD3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_5_2nd	ECOD (1.6)
A	SBP_bac_5_1st	e4ofoA1	A: a+b two layers	X: Alpha-beta plaits	H: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)	T: Oligo-peptide binding protein (OPPA) insertion domain	F: SBP_bac_5_1st	ECOD (1.6)
A	SBP_bac_5_3rd	e4ofoA2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_5_3rd	ECOD (1.6)
A	SBP_bac_5_2nd	e4ofoA3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_5_2nd	ECOD (1.6)
B	SBP_bac_5_1st	e4ofoB1	A: a+b two layers	X: Alpha-beta plaits	H: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)	T: Oligo-peptide binding protein (OPPA) insertion domain	F: SBP_bac_5_1st	ECOD (1.6)
B	SBP_bac_5_3rd	e4ofoB3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_5_3rd	ECOD (1.6)
B	SBP_bac_5_2nd	e4ofoB2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_5_2nd	ECOD (1.6)
C	SBP_bac_5_1st	e4ofoC1	A: a+b two layers	X: Alpha-beta plaits	H: Oligo-peptide binding protein (OPPA) insertion domain (From Topology)	T: Oligo-peptide binding protein (OPPA) insertion domain	F: SBP_bac_5_1st	ECOD (1.6)
C	SBP_bac_5_3rd	e4ofoC3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_5_3rd	ECOD (1.6)
C	SBP_bac_5_2nd	e4ofoC2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_5_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
D	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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, D	Extracytoplasmic Nickel-Binding Protein YpYntA	-	transmembrane transport localization transport cellular process establishment of localization	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000914	Solute-binding protein family 5 domain	Domain
A, B, C, D	IPR039424	Solute-binding protein family 5	Family
A, B, C, D	IPR030678	Peptide/nickel binding protein, MppA-type	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.