Annotations: 5IXM

The LPS Transporter LptDE from Yersinia pestis, core complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
H	SCOP2B Superfamily	TolB N-terminal domain-like	8053479	3000482	SCOP2B (2022-06-29)
F	SCOP2 Family	LptE-like	8045852	4004725	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	TolB N-terminal domain-like	8053479	3000482	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	TolB N-terminal domain-like	8053479	3000482	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TolB N-terminal domain-like	8053479	3000482	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	LptD-like barrel	8053494	3002195	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	LptD-like barrel	8053494	3002195	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LptD-like barrel	8053494	3002195	SCOP2B (2022-06-29)
A	SCOP2 Family	LptD C-terminal domain-like	8045951	4004780	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LptD-like barrel	8053494	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)
H	ANAPC1	e5ixmH1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: ANAPC1	ECOD (v295.2)
F	ANAPC1	e5ixmF1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: ANAPC1	ECOD (v295.2)
D	ANAPC1	e5ixmD1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: ANAPC1	ECOD (v295.2)
B	ANAPC1	e5ixmB1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: ANAPC1	ECOD (v295.2)
G	Capsid_NCLDV	e5ixmG1	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases	H: Alpha helical domain of ribonucleotide reductases	T: Alpha helical domain of ribonucleotide reductases	F: Capsid_NCLDV	ECOD (v295.2)
E	Capsid_NCLDV	e5ixmE1	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases	H: Alpha helical domain of ribonucleotide reductases	T: Alpha helical domain of ribonucleotide reductases	F: Capsid_NCLDV	ECOD (v295.2)
C	Capsid_NCLDV	e5ixmC1	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases	H: Alpha helical domain of ribonucleotide reductases	T: Alpha helical domain of ribonucleotide reductases	F: Capsid_NCLDV	ECOD (v295.2)
A	Capsid_NCLDV	e5ixmA1	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases	H: Alpha helical domain of ribonucleotide reductases	T: Alpha helical domain of ribonucleotide reductases	F: Capsid_NCLDV	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.160.150	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Lipoprotein like domain	CATH (4.3.0)
F	3.30.160.150	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Lipoprotein like domain	CATH (4.3.0)
D	3.30.160.150	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Lipoprotein like domain	CATH (4.3.0)
B	3.30.160.150	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Lipoprotein like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF04390	Lipopolysaccharide-assembly (LptE)	Lipopolysaccharide-assembly	-	Family
A, C, E, G	PF04453	LPS transport system D, C-terminal domain (LptD)	LPS transport system D, C-terminal domain	Lipopolysaccharide (LPS) is essential for most Gram-negative bacteria and has crucial roles in protection of the bacteria from harsh environments and toxic compounds, including antibiotics. This entry includes members such as LPTD found in Shigella f ...	Lipopolysaccharide (LPS) is essential for most Gram-negative bacteria and has crucial roles in protection of the bacteria from harsh environments and toxic compounds, including antibiotics. This entry includes members such as LPTD found in Shigella flexneri and Yersinia pestis. Structural analysis indicates that LptD forms a novel 26-stranded beta-barrel. It interacts with LPTE where LptE adopts a roll-like structure located inside the barrel of LptD. The LPS translocon LptD is unable to fold properly in the absence of LptE and the two proteins form a unique barrel and plug architecture for LPS transport and insertion [1,2]. LptD is an essential outer membrane protein that mediates the final transport of lipopolysaccharide (LPS) to outer leaflet. It has been suggested that LptD is a promising target for the development of effective vaccines and antibody-based therapies to control Vibrio infection [3]. This entry represents the C-terminal beta-barrel domain embedded in the outer membrane [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	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, C, E, G	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
B, D, F, H	IPR007485	LPS-assembly lipoprotein LptE	Family
A, C, E, G	IPR007543	LptD, C-terminal	Domain
A, C, E, G	IPR020889	LPS-assembly protein LptD	Family
A, C, E, G	IPR050218	Lipopolysaccharide Assembly Protein LptD	Family
A, C, E, G	IPR005653	Organic solvent tolerance-like, N-terminal	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H	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, C, D, E A, B, C, D, E, F, G, H	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

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