6VDF | pdb_00006vdf

Structure of the periplasmic domain of YejM from Salmonella typhimurium (twinned)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Arylsulfatase, C-terminal domain-like	8092298	3002305	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Alkaline phosphatase-like	8092296	3001353	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Alkaline phosphatase-like	8092296	3001353	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Arylsulfatase, C-terminal domain-like	8092298	3002305	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Alkaline phosphatase-like	8092296	3001353	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Arylsulfatase, C-terminal domain-like	8092298	3002305	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Alkaline phosphatase-like	8092296	3001353	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Arylsulfatase, C-terminal domain-like	8092298	3002305	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)
A	Pro_isomerase	e6vdfA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (develop294)
B	Pro_isomerase	e6vdfB1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (develop294)
C	Pro_isomerase	e6vdfC1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (develop294)
D	Pro_isomerase	e6vdfD1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00884	Sulfatase (Sulfatase)	Sulfatase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Periplasmic domain of the cardiolipin transporter protein YejM/PbgA	ion binding binding anion binding phosphatidylglycerol binding phospholipid binding lipid binding cardiolipin binding small molecule binding	membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization	cell periphery cellular anatomical structure plasma membrane membrane Gram-negative-bacterium-type cell wall external encapsulating structure cell envelope cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000917	Sulfatase, N-terminal	Domain
A, B, C, D	IPR012159	Inner membrane protein YejM-like	Family
A, B, C, D	IPR047997	Inner membrane protein YejM, enterobacterales	Family
A, B, C, D	IPR024588	Inner membrane protein YejM, N-terminal	Domain
A, B, C, D	IPR017850	Alkaline-phosphatase-like, core domain superfamily	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.