6HJY | pdb_00006hjy

X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) Delta8 truncation mutant in complex with nanobody 72

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
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)
I	d6hjyi_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
H	d6hjyh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
G	d6hjyg_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
J	d6hjyj1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
J	d6hjyj2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d6hjyf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d6hjyf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I	V-set_12	e6hjyI1	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)
H	V-set_12	e6hjyH1	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)
G	V-set_12	e6hjyG1	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)
J	V-set_8	e6hjyJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
F	V-set_8	e6hjyF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E	Neur_chan_LBD	e6hjyE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Nicotinic receptor ligand binding domain-like (From Topology)	T: Nicotinic receptor ligand binding domain-like	F: Neur_chan_LBD	ECOD (1.6)
E	Neur_chan_memb	e6hjyE1	A: alpha bundles	X: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	H: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	T: Neurotransmitter-gated ion-channel transmembrane pore	F: Neur_chan_memb	ECOD (1.6)
D	Neur_chan_LBD	e6hjyD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Nicotinic receptor ligand binding domain-like (From Topology)	T: Nicotinic receptor ligand binding domain-like	F: Neur_chan_LBD	ECOD (1.6)
D	Neur_chan_memb	e6hjyD1	A: alpha bundles	X: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	H: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	T: Neurotransmitter-gated ion-channel transmembrane pore	F: Neur_chan_memb	ECOD (1.6)
C	Neur_chan_LBD	e6hjyC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Nicotinic receptor ligand binding domain-like (From Topology)	T: Nicotinic receptor ligand binding domain-like	F: Neur_chan_LBD	ECOD (1.6)
C	Neur_chan_memb	e6hjyC1	A: alpha bundles	X: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	H: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	T: Neurotransmitter-gated ion-channel transmembrane pore	F: Neur_chan_memb	ECOD (1.6)
B	Neur_chan_LBD	e6hjyB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Nicotinic receptor ligand binding domain-like (From Topology)	T: Nicotinic receptor ligand binding domain-like	F: Neur_chan_LBD	ECOD (1.6)
B	Neur_chan_memb	e6hjyB1	A: alpha bundles	X: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	H: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	T: Neurotransmitter-gated ion-channel transmembrane pore	F: Neur_chan_memb	ECOD (1.6)
A	Neur_chan_LBD	e6hjyA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Nicotinic receptor ligand binding domain-like (From Topology)	T: Nicotinic receptor ligand binding domain-like	F: Neur_chan_LBD	ECOD (1.6)
A	Neur_chan_memb	e6hjyA2	A: alpha bundles	X: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	H: Neurotransmitter-gated ion-channel transmembrane pore (From Topology)	T: Neurotransmitter-gated ion-channel transmembrane pore	F: Neur_chan_memb	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G, H, I	Heavy Chain	IGHV1	-	cys-loop ligand-gated ion channel	SAbDab (2025-11-28)
F, J	Heavy Chain	IGHV1	-	cys-loop ligand-gated ion channel	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E	PF02931	Neurotransmitter-gated ion-channel ligand binding domain (Neur_chan_LBD)	Neurotransmitter-gated ion-channel ligand binding domain	-	Family
D	PF02931	Neurotransmitter-gated ion-channel ligand binding domain (Neur_chan_LBD)	Neurotransmitter-gated ion-channel ligand binding domain	-	Family
B, C	PF02931	Neurotransmitter-gated ion-channel ligand binding domain (Neur_chan_LBD)	Neurotransmitter-gated ion-channel ligand binding domain	-	Family
A	PF02931	Neurotransmitter-gated ion-channel ligand binding domain (Neur_chan_LBD)	Neurotransmitter-gated ion-channel ligand binding domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I	nanobody 72	-	-	-
F, J	nanobody 72	-	-	-
E	Cys-loop ligand-gated ion channel	ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity identical protein binding protein binding binding molecular transducer activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity identical protein binding protein binding binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	-	cell periphery cellular anatomical structure plasma membrane membrane
D	Cys-loop ligand-gated ion channel	ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity identical protein binding protein binding binding molecular transducer activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity identical protein binding protein binding binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	-	cell periphery cellular anatomical structure plasma membrane membrane
B, C	Cys-loop ligand-gated ion channel	ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity identical protein binding protein binding binding molecular transducer activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity identical protein binding protein binding binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	-	cell periphery cellular anatomical structure plasma membrane membrane
A	Cys-loop ligand-gated ion channel	ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity identical protein binding protein binding binding molecular transducer activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity identical protein binding protein binding binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	-	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E	IPR038050	Neuronal acetylcholine receptor	Homologous Superfamily
E	IPR006202	Neurotransmitter-gated ion-channel ligand-binding domain	Domain
E	IPR036719	Neurotransmitter-gated ion-channel transmembrane domain superfamily	Homologous Superfamily
E	IPR036734	Neurotransmitter-gated ion-channel ligand-binding domain superfamily	Homologous Superfamily
E	IPR006201	Neurotransmitter-gated ion-channel	Family
D	IPR038050	Neuronal acetylcholine receptor	Homologous Superfamily
D	IPR006202	Neurotransmitter-gated ion-channel ligand-binding domain	Domain
D	IPR036719	Neurotransmitter-gated ion-channel transmembrane domain superfamily	Homologous Superfamily
D	IPR036734	Neurotransmitter-gated ion-channel ligand-binding domain superfamily	Homologous Superfamily
D	IPR006201	Neurotransmitter-gated ion-channel	Family
B, C	IPR038050	Neuronal acetylcholine receptor	Homologous Superfamily
B, C	IPR006202	Neurotransmitter-gated ion-channel ligand-binding domain	Domain
B, C	IPR036719	Neurotransmitter-gated ion-channel transmembrane domain superfamily	Homologous Superfamily
B, C	IPR036734	Neurotransmitter-gated ion-channel ligand-binding domain superfamily	Homologous Superfamily
B, C	IPR006201	Neurotransmitter-gated ion-channel	Family
A	IPR038050	Neuronal acetylcholine receptor	Homologous Superfamily
A	IPR006202	Neurotransmitter-gated ion-channel ligand-binding domain	Domain
A	IPR036719	Neurotransmitter-gated ion-channel transmembrane domain superfamily	Homologous Superfamily
A	IPR036734	Neurotransmitter-gated ion-channel ligand-binding domain superfamily	Homologous Superfamily
A	IPR006201	Neurotransmitter-gated ion-channel	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E	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	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Cys-Loop Receptor Family	Prokaryotic pentameric ligand-gated ion channel, 7'C pore mutant (L238C)