6R8A | pdb_00006r8a

Structure of Arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-methionine

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d6r8ad_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ], thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d6r8ac_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ], thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d6r8ab_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ], thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d6r8aa_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ], thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	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	SBP_bac_3_1st	e6r8aD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_3_1st	ECOD (1.6)
D	UNK_F_TYPE	e6r8aD2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: UNK_F_TYPE	ECOD (1.6)
C	SBP_bac_3_1st	e6r8aC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_3_1st	ECOD (1.6)
C	UNK_F_TYPE	e6r8aC2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: UNK_F_TYPE	ECOD (1.6)
B	SBP_bac_3_1st	e6r8aB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_3_1st	ECOD (1.6)
B	UNK_F_TYPE	e6r8aB2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: UNK_F_TYPE	ECOD (1.6)
A	SBP_bac_3_1st	e6r8aA2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_3_1st	ECOD (1.6)
A	UNK_F_TYPE	e6r8aA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: UNK_F_TYPE	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
A, B, C, D	PF10613	Ligated ion channel L-glutamate- and glycine-binding site (Lig_chan-Glu_bd)	Ligated ion channel L-glutamate- and glycine-binding site	This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, Pfam:PF ...	This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, Pfam:PF00060.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Glutamate receptor 3.3,Glutamate receptor 3.3	ligand-gated channel activity 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 glutamate receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity calcium channel activity ligand-gated channel activity 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 glutamate receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity calcium channel activity monoatomic cation transmembrane transporter activity monoatomic cation channel activity calcium ion transmembrane transporter activity metal ion transmembrane transporter activity	response to stimulus response to abiotic stimulus tropism response to external stimulus gravitropism response to gravity cellular response to acid chemical cellular response to stimulus cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to chemical cellular process response to amino acid response to stimulus response to abiotic stimulus tropism response to external stimulus gravitropism response to gravity cellular response to acid chemical cellular response to stimulus cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to chemical cellular process response to amino acid response to stress response to wounding defense response to fungus biological process involved in interspecies interaction between organisms response to other organism defense response response to fungus response to external biotic stimulus response to biotic stimulus localization transport monoatomic ion transport monoatomic cation transport establishment of localization calcium ion transport metal ion transport immune response defense response to symbiont immune system process defense response to other organism innate immune response regulation of biological process signaling biological regulation cell-cell signaling cell communication regulation of cellular process intracellular signal transduction calcium-mediated signaling intracellular signaling cassette signal transduction positive regulation of response to biotic stimulus induced systemic resistance, jasmonic acid mediated signaling pathway positive regulation of immune response response to hormone response to bacterium regulation of immune system process positive regulation of immune system process cellular response to hormone stimulus response to jasmonic acid regulation of innate immune response response to fatty acid jasmonic acid mediated signaling pathway cellular response to oxygen-containing compound immune effector process cellular response to fatty acid regulation of response to stimulus cellular response to lipid positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response regulation of defense response regulation of response to biotic stimulus regulation of response to external stimulus response to lipid positive regulation of biological process hormone-mediated signaling pathway positive regulation of response to stimulus defense response to bacterium cellular response to endogenous stimulus positive regulation of response to external stimulus cellular response to jasmonic acid stimulus regulation of response to stress positive regulation of innate immune response response to endogenous stimulus response to oxygen-containing compound induced systemic resistance	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017103	Ionotropic glutamate receptor, plant	Family
A, B, C, D	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, B, C, D	IPR044440	Plant glutamate receptor, periplasmic ligand-binding domain	Domain
A, B, C, D	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF	Domain
A, B, C, D	IPR015683	Ionotropic glutamate receptor	Family
A, B, C, D	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A, B, C, D	IPR001828	Receptor, ligand binding region	Domain

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.