Annotations: 7RXC

CryoEM structure of KDELR with Legobody

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2 Family	Phosphate binding protein-like	8105368	4000229	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Family	Immunoglobulin-binding protein A modules	8105460	4000790	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Superfamily	Type 2 solute binding protein-like	8105369	3000083	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Superfamily	Bacterial immunoglobulin/albumin-binding domains	8105461	3001373	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 [auth L]	G-gamma	e7rxcL1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: G-gamma	ECOD (v294.2)
D [auth B]	SBP_bac_1	e7rxcB1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_1	ECOD (v294.2)
D [auth B]	Sybindin	e7rxcB2	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Sybindin	ECOD (v294.2)
C [auth N]	G-gamma	e7rxcN1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: G-gamma	ECOD (v294.2)
A [auth H]	G-gamma	e7rxcH1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: G-gamma	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth B]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
C [auth N]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L]	Light Chain	IGKV8	Kappa	maltodextrin-binding protein,immunoglobulin g-bindingprotein a,immunoglobulin g-binding protein g	SAbDab (2026-05-08)
C [auth N]	Heavy Chain	IGHV1	-	er lumen protein-retaining receptor 2	SAbDab (2026-05-08)
A [auth H]	Heavy Chain	IGHV5	-	maltodextrin-binding protein,immunoglobulin g-bindingprotein a,immunoglobulin g-binding protein g	SAbDab (2026-05-08)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth K]	PF00810	ER lumen protein retaining receptor (ER_lumen_recept)	ER lumen protein retaining receptor	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth L]	Fab_8D3_2 light chain	-	-	-
E [auth K]	ER lumen protein-retaining receptor 2	signal sequence binding binding ER retention sequence binding peptide binding KDEL sequence binding	maintenance of protein location cellular localization maintenance of location maintenance of location in cell localization maintenance of protein localization in endoplasmic reticulum maintenance of protein location in cell macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle intracellular protein localization protein localization to endoplasmic reticulum protein retention in ER lumen maintenance of protein location cellular localization maintenance of location maintenance of location in cell localization maintenance of protein localization in endoplasmic reticulum maintenance of protein location in cell macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle intracellular protein localization protein localization to endoplasmic reticulum protein retention in ER lumen transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum establishment of localization Golgi vesicle transport vesicle-mediated transport establishment of protein localization protein transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm endomembrane system membrane intracellular vesicle COPI-coated vesicle COPI-coated vesicle membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm endomembrane system membrane intracellular vesicle COPI-coated vesicle COPI-coated vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle coated vesicle membrane vesicle membrane cytoplasmic vesicle Golgi-associated vesicle membrane coated vesicle Golgi-associated vesicle vesicle organelle membrane Golgi membrane endoplasmic reticulum organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane
D [auth B]	Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G	protein-containing complex binding binding immunoglobulin binding IgG binding	-	-
C [auth N]	Nb_KR	-	-	-
A [auth H]	Fab_8D3_2 heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth K]	IPR000133	ER lumen protein retaining receptor	Family
D [auth B]	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
D [auth B]	IPR005877	YSIRK Gram-positive signal peptide	Domain
D [auth B]	IPR000724	IgG-binding B	Domain
D [auth B]	IPR019950	M protein-type anchor motif	Conserved Site
D [auth B]	IPR035152	GA-like domain	Domain
D [auth B]	IPR019931	LPXTG cell wall anchor motif	Conserved Site
D [auth B]	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
D [auth B]	IPR005877	YSIRK Gram-positive signal peptide	Domain
D [auth B]	IPR036779	LysM domain superfamily	Homologous Superfamily
D [auth B]	IPR005038	Octapeptide repeat	Repeat
D [auth B]	IPR003132	Protein A, Ig-binding domain	Domain
D [auth B]	IPR018392	LysM domain	Domain
D [auth B]	IPR019931	LPXTG cell wall anchor motif	Conserved Site

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
D [auth B], E [auth K]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
D [auth B], E [auth K]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	SWEET and semiSWEET Transporters, and Their Relatives	KDEL receptor with bound nanobody-binding scaffold (Legobody)

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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.