3NCY

X-ray crystal structure of an arginine agmatine antiporter (AdiC) in complex with a Fab fragment

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Arginine/agmatine antiporter-like	8048865	4006243	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SNF-like	8092927	3001654	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	SNF-like	8092927	3001654	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SNF-like	8092927	3001654	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SNF-like	8092927	3001654	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	AA_permease_2_1	e3ncyA1	A: alpha complex topology	X: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	H: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	T: Sodium:neurotransmitter symporter family (SNF)-like	F: AA_permease_2_1	ECOD (1.6)
B	AA_permease_2_1	e3ncyB1	A: alpha complex topology	X: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	H: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	T: Sodium:neurotransmitter symporter family (SNF)-like	F: AA_permease_2_1	ECOD (1.6)
C	AA_permease_2_1	e3ncyC1	A: alpha complex topology	X: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	H: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	T: Sodium:neurotransmitter symporter family (SNF)-like	F: AA_permease_2_1	ECOD (1.6)
D	AA_permease_2_1	e3ncyD1	A: alpha complex topology	X: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	H: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	T: Sodium:neurotransmitter symporter family (SNF)-like	F: AA_permease_2_1	ECOD (1.6)
E [auth Q]	V-set_8	e3ncyQ1	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 [auth Q]	C1-set_1	e3ncyQ2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
F [auth P]	V-set_8	e3ncyP1	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 [auth P]	C1-set_1	e3ncyP2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
G [auth W]	C1-set_4	e3ncyW2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
G [auth W]	V-set	e3ncyW1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
H [auth S]	C1-set_4	e3ncyS2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
H [auth S]	V-set	e3ncyS1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth Q]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth P]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth W]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth S]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
E [auth Q], F [auth P]	Antibody Fab Fragment	VH-CH1	Mus musculus (house mouse)	IGHV1S1201, IGHV1S5601, IGHV1-7501, IGHJ401, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202507-0)
G [auth W], H [auth S]	Antibody Fab Fragment	L-KAPPA	Mus musculus (house mouse)	IGKV4-5901, IGKJ101, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202507-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth Q], F [auth P]	Heavy Chain	IGHV1	-	adic \| adic	SAbDab (2025-02-28)
G [auth W], H [auth S]	Light Chain	IGKV4	Kappa	adic \| adic	SAbDab (2025-02-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13520	Amino acid permease (AA_permease_2)	Amino acid permease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	AdiC	antiporter activity active transmembrane transporter activity transporter activity transmembrane transporter activity secondary active transmembrane transporter activity identical protein binding protein binding binding	amino acid transport localization transport establishment of localization	cell periphery cellular anatomical structure plasma membrane membrane
E [auth Q], F [auth P]	Fab Heavy chain	-	-	-
G [auth W], H [auth S]	Fab Light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002293	Amino acid/polyamine transporter I	Family
A, B, C, D	IPR050367	Amino acid-polyamine-organocation superfamily	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Amino Acid/Polyamine/Organocation (APC) Superfamily	AdiC Arginine:Agmatine Antiporter (with Fab fragment)

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.