9Q8N | pdb_00009q8n

Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 16)

External Resource: Annotation

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

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	8053486	3000482	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LptD-like barrel	8053497	3002195	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF04390	Lipopolysaccharide-assembly (LptE)	Lipopolysaccharide-assembly	-	Family
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
C	Compound 16 - Bicyclic Peptide Binder	-	-	-
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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

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.