6ZPL | pdb_00006zpl

Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
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)
C	SCOP2B Superfamily	(Trans)glycosidases	8037148	3000313	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)
D [auth E]	Raptor_N	e6zplE1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Raptor_N	ECOD (v294.1)
E [auth F]	Raptor_N	e6zplF1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Raptor_N	ECOD (v294.1)
C	Head-tail_con	e6zplC1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Head-tail_con	ECOD (v294.1)
B [auth A]	Raptor_N	e6zplA1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Raptor_N	ECOD (v294.1)
A [auth B]	Raptor_N	e6zplB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Raptor_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF02156	Glycosyl hydrolase family 26 (Glyco_hydro_26)	Glycosyl hydrolase family 26		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth E], E [auth F]	Sybody Sb_GlyT1#7	-	-	-
C	Endoglucanase H	hydrolase activity, acting on glycosyl bonds glucosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity beta-glucosidase activity catalytic activity cellulase activity	carbohydrate metabolic process catabolic process glucan catabolic process beta-glucan metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process beta-glucan catabolic process polysaccharide catabolic process metabolic process cellular process cellulose catabolic process carbohydrate metabolic process catabolic process glucan catabolic process beta-glucan metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process beta-glucan catabolic process polysaccharide catabolic process metabolic process cellular process cellulose catabolic process macromolecule metabolic process cellulose metabolic process	cellular anatomical structure extracellular region cell surface
A [auth B], B [auth A]	Sodium- and chloride-dependent glycine transporter 1	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 amino acid transmembrane transporter activity active 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 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 amino acid transmembrane transporter activity active 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 glycine transmembrane transporter activity carboxylic acid transmembrane transporter activity glycine:sodium symporter activity neutral L-amino acid:sodium symporter activity organic acid:sodium symporter activity neutral L-amino acid transmembrane transporter activity	import into cell organic anion transport nitrogen compound transport glycine import across plasma membrane carboxylic acid transmembrane transport carboxylic acid transport transport glycine transport import across plasma membrane neutral amino acid transport amino acid transmembrane transport establishment of localization organic cation transport transmembrane transport organic acid transport import into cell organic anion transport nitrogen compound transport glycine import across plasma membrane carboxylic acid transmembrane transport carboxylic acid transport transport glycine transport import across plasma membrane neutral amino acid transport amino acid transmembrane transport establishment of localization organic cation transport transmembrane transport organic acid transport amino acid transport localization cellular process amino acid import across plasma membrane trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process signaling modulation of chemical synaptic transmission regulation of synaptic transmission, glycinergic biological regulation cell-cell signaling synaptic transmission, glycinergic chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication neurotransmitter uptake neurotransmitter transport positive regulation of protein metabolic process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of hemoglobin biosynthetic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process hemoglobin metabolic process regulation of biosynthetic process hemoglobin biosynthetic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule biosynthetic process biosynthetic process regulation of hemoglobin biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process monoatomic ion transmembrane transport sodium ion transmembrane transport metal ion transport monoatomic cation transmembrane transport monoatomic ion transport monoatomic cation transport sodium ion transport cellular localization secretion by cell signal release establishment of localization in cell neurotransmitter secretion secretion glycine secretion export from cell signal release from synapse glycine secretion, neurotransmission heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process heme biosynthetic process pigment biosynthetic process positive regulation of tetrapyrrole biosynthetic process tetrapyrrole biosynthetic process regulation of tetrapyrrole biosynthetic process porphyrin-containing compound metabolic process positive regulation of heme biosynthetic process tetrapyrrole metabolic process regulation of heme biosynthetic process regulation of tetrapyrrole metabolic process multicellular organismal process system process circulatory system process vascular process in circulatory system vascular transport transport across blood-brain barrier	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane apical part of cell apical plasma membrane basal part of cell basal plasma membrane cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane apical part of cell apical plasma membrane basal part of cell basal plasma membrane parallel fiber to Purkinje cell synapse excitatory synapse presynapse presynaptic membrane basolateral plasma membrane membrane-bounded organelle intracellular anatomical structure dense core granule intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle neuron to neuron synapse hippocampal mossy fiber to CA3 synapse endosome postsynaptic density postsynaptic specialization asymmetric synapse transport vesicle membrane bounding membrane of organelle vesicle membrane synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane organelle membrane exocytic vesicle lateral plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR002105	Dockerin type I repeat	Repeat
C	IPR005087	Carbohydrate binding module family 11	Domain
C	IPR016134	Dockerin domain	Domain
C	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
C	IPR001547	Glycoside hydrolase, family 5	Domain
C	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
C	IPR050386	Glycosyl Hydrolase 5 (Cellulase A)	Family
C	IPR036439	Dockerin domain superfamily	Homologous Superfamily
C	IPR022790	Glycosyl hydrolase family 26 domain	Domain
C	IPR018087	Glycoside hydrolase, family 5, conserved site	Conserved Site
A [auth B], B [auth A]	IPR000175	Sodium:neurotransmitter symporter	Family
A [auth B], B [auth A]	IPR003028	Sodium:neurotransmitter symporter, glycine, type 1	Family
A [auth B], B [auth A]	IPR037272	Sodium:neurotransmitter symporter superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], B [auth A]	Pharos: P48067	atypical glycine encephalopathy amphetamine abuse Alcoholic Intoxication, Chronic intellectual disability MALT lymphoma polycystic ovary syndrome schizophrenia astrocytic tumor cutaneous lupus erythematosus malignant ependymoma psoriasis attention deficit hyperactivity disorder, inattentive type glioblastoma malignant glioma oligodendroglioma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth B], B [auth A], C	OPM	Transmembrane	Alpha-helical polytopic	APC (Amino acid-Polyamine-organoCation) superfamily	Neurotransmitter: sodium symporter

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth B], B [auth A], C	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth B], B [auth A], C	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth B], B [auth A], C	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Solute Carrier (SLC) Transporter Superfamily	glycine transporter 1 (GlyT1), inward-open state in complex with a benzoylisoindoline inhibitor

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.