6CSF

Crystal structure of sodium/alanine symporter AgcS with D-alanine bound

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	C1-set_1	e6csfA1	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)
A	V-set_12	e6csfA2	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)
D [auth H]	C1-set_1	e6csfH1	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)
D [auth H]	V-set_12	e6csfH2	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)
B	C1-set_4	e6csfB2	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)
B	V-set	e6csfB1	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)
F [auth L]	C1-set_4	e6csfL1	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)
F [auth L]	V-set	e6csfL2	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)
C [auth M]	UNK_F_TYPE	e6csfM1	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: UNK_F_TYPE	ECOD (1.6)
E [auth C]	UNK_F_TYPE	e6csfC1	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: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth L]	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
A, D [auth H]	Antibody Fab Fragment	VH-CH1	Mus musculus (house mouse)	IGHV6-601, IGHJ103, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B, F [auth L]	Antibody Fab Fragment	L-KAPPA	Mus musculus (house mouse)	IGKV12-4401, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D [auth H]	Heavy Chain	IGHV6	-	sodium/alanine symporter agcs	SAbDab (2024-04-19)
B, F [auth L]	Light Chain	IGKV12	Kappa	sodium/alanine symporter agcs	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth M], E [auth C]	PF01235	Sodium:alanine symporter family (Na_Ala_symp)	Sodium:alanine symporter family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth H]	Monoclonal antibody FAB heavy chain	-	-	-
B, F [auth L]	Monoclonal antibody FAB light chain	-	-	-
C [auth M], E [auth C]	Sodium/alanine symporter AgcS	monoatomic cation transmembrane transporter activity amino acid:sodium symporter activity solute:sodium symporter activity solute:monoatomic cation symporter activity sodium ion transmembrane transporter activity secondary active transmembrane transporter activity active monoatomic ion transmembrane transporter activity amino acid transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity amino acid:monoatomic cation symporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity monoatomic cation transmembrane transporter activity amino acid:sodium symporter activity solute:sodium symporter activity solute:monoatomic cation symporter activity sodium ion transmembrane transporter activity secondary active transmembrane transporter activity active monoatomic ion transmembrane transporter activity amino acid transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity amino acid:monoatomic cation symporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity symporter activity	-	cell periphery plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth M], E [auth C]	IPR001463	Sodium:alanine symporter	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
C [auth M], E [auth C]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
C [auth M], E [auth C]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
C [auth M], E [auth C]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Amino Acid/Polyamine/Organocation (APC) Superfamily	AgcS sodium/alanine symporter with bound L-alanine

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.