6C08 | pdb_00006c08

Zebrafish SLC38A9 with arginine bound in the cytosol open state

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
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)
D	d6c08d_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d6c08a_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d6c08b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d6c08e1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	V-set_8	e6c08D1	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)
D	C1-set_1	e6c08D2	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_8	e6c08A2	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)
A	C1-set_1	e6c08A1	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)
C	UNK_F_TYPE	e6c08C1	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)
F	UNK_F_TYPE	e6c08F1	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)
B	C1-set_4	e6c08B2	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	e6c08B1	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)
E	C1-set_4	e6c08E2	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)
E	V-set	e6c08E1	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)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	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	Antibody Fab Fragment	VH-CH1	Mus musculus (house mouse)	IGHV9-2-101, IGHV9-302, IGHV9-3-101, IGHJ401, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	(VH-CH1)_L-KAPPA	IMGT (202549-0)
B, E	Antibody Fab Fragment	L-KAPPA	Mus musculus (house mouse)	IGKV19-9301, IGKV19-9302, IGKJ101, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	(VH-CH1)_L-KAPPA	IMGT (202549-0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	antibody Fab Heavy Chain	-	-	-
C, F	Sodium-coupled neutral amino acid transporter 9	L-arginine transmembrane transporter activity L-amino acid transmembrane transporter activity amino acid transmembrane transporter activity transporter activity carboxylic acid transmembrane transporter activity basic amino acid transmembrane transporter activity transmembrane transporter activity sterol binding binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding L-arginine transmembrane transporter activity L-amino acid transmembrane transporter activity amino acid transmembrane transporter activity transporter activity carboxylic acid transmembrane transporter activity basic amino acid transmembrane transporter activity transmembrane transporter activity sterol binding binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding L-glutamine transmembrane transporter activity neutral L-amino acid transmembrane transporter activity cation binding organic acid binding ion binding anion binding amino acid binding carboxylic acid binding arginine binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity amino acid sensor activity molecular sensor activity L-leucine transmembrane transporter activity branched-chain amino acid transmembrane transporter activity L-asparagine transmembrane transporter activity amide transmembrane transporter activity metal ion binding lipid sensor activity sterol sensor activity	organic anion transport nitrogen compound transport carboxylic acid transmembrane transport carboxylic acid transport transport amino acid transmembrane transport L-amino acid transport establishment of localization organic cation transport basic amino acid transmembrane transport L-arginine transmembrane transport transmembrane transport organic acid transport amino acid transport localization organic anion transport nitrogen compound transport carboxylic acid transmembrane transport carboxylic acid transport transport amino acid transmembrane transport L-amino acid transport establishment of localization organic cation transport basic amino acid transmembrane transport L-arginine transmembrane transport transmembrane transport organic acid transport amino acid transport localization basic amino acid transport L-alpha-amino acid transmembrane transport cellular process monosaccharide metabolic process regulation of cellular process gluconeogenesis regulation of primary metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process carbohydrate biosynthetic process biological regulation hexose metabolic process primary metabolic process monosaccharide biosynthetic process hexose biosynthetic process biosynthetic process regulation of gluconeogenesis metabolic process regulation of carbohydrate biosynthetic process regulation of metabolic process glucose metabolic process asparagine transport neutral amino acid transport cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of signaling ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process organophosphate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy nucleoside phosphate catabolic process organic acid metabolic process regulation of ATP metabolic process nucleobase-containing compound metabolic process regulation of purine nucleotide catabolic process glycolytic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process regulation of nucleobase-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process regulation of carbohydrate catabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of nucleotide catabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration catabolic process ATP metabolic process energy derivation by oxidation of organic compounds purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process regulation of catabolic process generation of precursor metabolites and energy regulation of glycolytic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process amino acid metabolic process positive regulation of TORC1 signaling regulation of TORC1 signaling TORC1 signaling response to decreased oxygen levels regulation of cellular response to hypoxia cellular response to oxygen levels cellular response to hypoxia regulation of cellular response to stress cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia regulation of response to stress response to stress response to chemical response to oxygen levels response to abiotic stimulus cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid L-leucine transport branched-chain amino acid transport glutamine transport	cellular anatomical structure membrane membrane-bounded organelle endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle cellular anatomical structure membrane membrane-bounded organelle endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle late endosome cytoplasm vesicle organelle membrane lytic vacuole vacuole lysosome vacuolar membrane lytic vacuole membrane lysosomal membrane
B, E	antibody Fab light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR013057	Amino acid transporter, transmembrane domain	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
C, F	OPM	Transmembrane	Alpha-helical polytopic	APC (Amino acid-Polyamine-organoCation) superfamily	Amino acid/auxin permease

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
C, F	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
C, F	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
C, F	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Solute Carrier (SLC) Transporter Superfamily	SLC38A9 lysosomal amino acid transporter, cytosol-open state

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.