4OFO | pdb_00004ofo

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	Epimerase, NmrA	e4ofoD1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (v294.1)
D	SBP_bac_1	e4ofoD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v294.1)
C	Epimerase, NmrA	e4ofoC1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (v294.1)
C	SBP_bac_1	e4ofoC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v294.1)
B	Epimerase, NmrA	e4ofoB1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (v294.1)
B	SBP_bac_1	e4ofoB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v294.1)
A	Epimerase, NmrA	e4ofoA1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (v294.1)
A	SBP_bac_5	e4ofoA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_5	ECOD (v294.1)

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)
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, 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	peptide transmembrane transporter activity transporter activity transmembrane transporter activity	peptide transport localization transport 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 extracellular region outer membrane-bounded periplasmic space cell envelope 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 extracellular region 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.