6C9W

Crystal Structure of a ligand bound LacY/Nanobody Complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6c9wa_	Membrane and cell surface proteins and peptides	MFS general substrate transporter	MFS general substrate transporter	LacY-like proton/sugar symporter	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d6c9wb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	MFS general substrate transporter	8039139	3000310	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	LacY_symp	e6c9wA1	A: alpha complex topology	X: Major facilitator superfamily (MFS) general substrate transporter (From Topology)	H: Major facilitator superfamily (MFS) general substrate transporter (From Topology)	T: Major facilitator superfamily (MFS) general substrate transporter	F: LacY_symp	ECOD (1.6)
B	V-set_12	e6c9wB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1250.20	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV1	-	lactose permease	SAbDab (2024-08-16)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Lactose permease	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity solute:monoatomic cation symporter activity disaccharide transmembrane transporter activity oligosaccharide transmembrane transporter activity secondary active transmembrane transporter activity lactose:proton symporter activity carbohydrate:monoatomic cation symporter activity active monoatomic ion transmembrane transporter activity carbohydrate:proton symporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity solute:proton symporter activity inorganic cation transmembrane transporter activity lactose transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity solute:monoatomic cation symporter activity disaccharide transmembrane transporter activity oligosaccharide transmembrane transporter activity secondary active transmembrane transporter activity lactose:proton symporter activity carbohydrate:monoatomic cation symporter activity active monoatomic ion transmembrane transporter activity carbohydrate:proton symporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity solute:proton symporter activity inorganic cation transmembrane transporter activity lactose transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity symporter activity oligosaccharide binding lactose binding binding disaccharide binding carbohydrate binding	localization transport carbohydrate transport establishment of localization lactose transport oligosaccharide transport disaccharide transport	cell periphery plasma membrane membrane cellular anatomical entity
B	Nanobody9047	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR018457	LacY/RafB permease family, conserved site	Conserved Site
A	IPR036259	MFS transporter superfamily	Homologous Superfamily
A	IPR000576	LacY/RafB permease family	Family
A	IPR020846	Major facilitator superfamily domain	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Transmembrane	Alpha-helical polytopic	Major Facilitator Superfamily (MFS)	LacY-like proton/sugar symporter

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Major Facilitator Superfamily (MFS) Transporters	LacY Lactose Permease Transporter (G46W, G262W mutant) with bound nanobody Nb9047 in complex with NPG

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 R01GM133198.