5IV9 | pdb_00005iv9

The LPS Transporter LptDE from Klebsiella pneumoniae, full-length

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
AMR Gene: CARD Annotation
AMR Gene Family: CARD Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	TolB N-terminal domain-like	8053482	3000482	SCOP2B (2022-06-29)
A	SCOP2 Family	LptA-like	8045264	4004381	SCOP2 (2022-06-29)
A	SCOP2 Family	LptD C-terminal domain-like	8045952	4004780	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	OstA-like beta-folder	8053500	3002196	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LptD-like barrel	8053498	3002195	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	LptE	e5iv9B1	A: a/b three-layered sandwiches	X: TolB, N-terminal domain (From Topology)	H: TolB, N-terminal domain (From Topology)	T: TolB, N-terminal domain	F: LptE	ECOD (1.6)
A	OstA_C	e5iv9A1	A: beta barrels	X: Outer membrane meander beta-barrels	H: LPS-assembly protein LptD (From Topology)	T: LPS-assembly protein LptD	F: OstA_C	ECOD (1.6)
A	OstA	e5iv9A2	A: beta meanders	X: Periplasmic lipopolysaccharide transport protein LptA (YhbN) (From Topology)	H: Periplasmic lipopolysaccharide transport protein LptA (YhbN) (From Topology)	T: Periplasmic lipopolysaccharide transport protein LptA (YhbN)	F: OstA	ECOD (1.6)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A	ARO:3005059	LptD	LptD is involved in LPS transport in a ABC Transporter efflux system. It confers resistance to rifamycin, aminocoumarin, and peptide antibiotics.	CARD (4.0.1)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A	ARO:0010001	ATP-binding cassette (ABC) antibiotic efflux pump	carbapenem, peptide antibiotic, aminocoumarin antibiotic, rifamycin antibiotic	antibiotic efflux	CARD (4.0.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF04390	Lipopolysaccharide-assembly (LptE)	Lipopolysaccharide-assembly	-	Family
A	PF03968	LptA/(LptD N-terminal domain) LPS transport protein (LptD_N)	LptA/(LptD N-terminal domain) LPS transport protein	This family of proteins are involved in lipopolysaccharide transport across the gram negative inner and outer membranes. The type examples for this family are E. coli LptA Swiss:P0ADV1 and the N-terminal domain of LptD Swiss:P31554.	Domain
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
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 periphery cell outer membrane cellular anatomical structure external encapsulating structure membrane cell envelope outer membrane
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 periphery cell outer membrane cellular anatomical structure external encapsulating structure membrane cell envelope outer membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR007485	LPS-assembly lipoprotein LptE	Family
A	IPR007543	LptD, C-terminal	Domain
A	IPR020889	LPS-assembly protein LptD	Family
A	IPR050218	Lipopolysaccharide Assembly Protein LptD	Family
A	IPR005653	Organic solvent tolerance-like, N-terminal	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Beta-barrel transmembrane	LPS assembly protein family (n=26, S=30)	LPS assembly protein family (n=26, S=30)

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Lipopolysaccharide (LPS) Transport Proteins	LptD-LptE lipopolysaccharide transport complex

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.