9RPW | pdb_00009rpw

Cryo-EM structure of Shigella flexneri LptDE dimer: closed-state unbound and open-state bound by Oekolampad phage RBP

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)
D [auth B]	SCOP2B Superfamily	TolB N-terminal domain-like	8053486	3000482	SCOP2B (2022-06-29)
B [auth E]	SCOP2B Superfamily	TolB N-terminal domain-like	8053486	3000482	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	LptD-like barrel	8053497	3002195	SCOP2B (2022-06-29)
A [auth D]	SCOP2B Superfamily	LptD-like barrel	8053497	3002195	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)
D [auth B]	RVT_1	e9rpwB1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: RVT_1	ECOD (v295.2)
B [auth E]	RVT_1	e9rpwE1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: RVT_1	ECOD (v295.2)
C [auth A]	IBR	e9rpwA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
A [auth D]	IBR	e9rpwD1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth E], D [auth B]	PF04390	Lipopolysaccharide-assembly (LptE)	Lipopolysaccharide-assembly	-	Family
A [auth D], C [auth A]	PF04453	LPS transport system D (LptD)	LPS transport system D	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth C]	Tail fiber protein	-	-	-
B [auth E], D [auth B]	LPS-assembly lipoprotein LptE	binding lipid binding lipopolysaccharide binding carbohydrate derivative 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 localization transport lipopolysaccharide transport 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 localization transport lipopolysaccharide transport macromolecule localization lipid localization lipid transport carbohydrate derivative transport establishment of localization	protein-containing complex transporter complex cell outer membrane cellular anatomical structure external encapsulating structure extracellular region membrane cell envelope outer membrane
A [auth D], C [auth A]	LPS-assembly protein LptD	-	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 localization transport lipopolysaccharide transport 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 localization transport lipopolysaccharide transport macromolecule localization lipid localization lipid transport carbohydrate derivative transport establishment of localization	protein-containing complex transporter complex cell outer membrane cellular anatomical structure external encapsulating structure extracellular region membrane cell envelope outer membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth C]	IPR045604	Domain of unknown function DUF6453	Domain
B [auth E], D [auth B]	IPR007485	LPS-assembly lipoprotein LptE	Family
A [auth D], C [auth A]	IPR007543	LptD, C-terminal	Domain
A [auth D], C [auth A]	IPR020889	LPS-assembly protein LptD	Family
A [auth D], C [auth A]	IPR050218	Lipopolysaccharide Assembly Protein LptD	Family
A [auth D], C [auth A]	IPR005653	Organic solvent tolerance-like, N-terminal	Domain

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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.