5IPV

Cryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV-bound conformation, state 1

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
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	F_UNCLASSIFIED	e5ipvA5	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF01094	e5ipvA4	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF01094	ECOD (1.6)
A	F_UNCLASSIFIED	e5ipvA3	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: F_UNCLASSIFIED	ECOD (1.6)
A	PF10613	e5ipvA2	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: PF10613	ECOD (1.6)
C	F_UNCLASSIFIED	e5ipvC5	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF01094	e5ipvC4	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF01094	ECOD (1.6)
C	F_UNCLASSIFIED	e5ipvC3	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: F_UNCLASSIFIED	ECOD (1.6)
C	PF10613	e5ipvC2	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: PF10613	ECOD (1.6)
B	F_UNCLASSIFIED	e5ipvB3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF01094	e5ipvB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF01094	ECOD (1.6)
B	F_UNCLASSIFIED	e5ipvB4	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: F_UNCLASSIFIED	ECOD (1.6)
B	PF10613	e5ipvB5	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: PF10613	ECOD (1.6)
D	F_UNCLASSIFIED	e5ipvD3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF01094	e5ipvD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF01094	ECOD (1.6)
D	F_UNCLASSIFIED	e5ipvD2	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: F_UNCLASSIFIED	ECOD (1.6)
D	PF10613	e5ipvD4	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: PF10613	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF01094	Receptor family ligand binding region (ANF_receptor)	Receptor family ligand binding region	-	Family
A, C	PF00497	Bacterial extracellular solute-binding proteins, family 3 (SBP_bac_3)	Bacterial extracellular solute-binding proteins, family 3	This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. Th ...	This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognises Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate [1].	Domain
B, D	PF01094	Receptor family ligand binding region (ANF_receptor)	Receptor family ligand binding region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	N-methyl-D-aspartate receptor subunit NR1-8a	transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity glutamate receptor activity gated channel activity signaling receptor activity carboxylic acid transmembrane transporter activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transmitter-gated channel activity organic acid transmembrane transporter activity transmembrane transporter activity organic anion transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	response to stimulus response to metal ion response to chemical response to zinc ion response to inorganic substance	cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane protein-containing complex plasma membrane protein complex membrane protein complex transporter complex cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane protein-containing complex plasma membrane protein complex membrane protein complex transporter complex NMDA selective glutamate receptor complex receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex
B, D	Ionotropic glutamate receptor subunit NR2B	transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity glutamate receptor activity gated channel activity signaling receptor activity carboxylic acid transmembrane transporter activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transmitter-gated channel activity organic acid transmembrane transporter activity transmembrane transporter activity organic anion transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	response to stimulus response to metal ion response to chemical response to zinc ion response to inorganic substance response to magnesium ion	cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane protein-containing complex plasma membrane protein complex membrane protein complex transporter complex cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane protein-containing complex plasma membrane protein complex membrane protein complex transporter complex NMDA selective glutamate receptor complex receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle late endosome cytoplasm vesicle lytic vacuole vacuole lysosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, C	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF	Domain
A, C	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A, C	IPR015683	Ionotropic glutamate receptor	Family
A, C	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A, C	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A, C	IPR001828	Receptor, ligand binding region	Domain
B, D	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
B, D	IPR018884	Glutamate [NMDA] receptor, epsilon subunit, C-terminal	Domain
B, D	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF	Domain
B, D	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
B, D	IPR015683	Ionotropic glutamate receptor	Family
B, D	IPR001508	Ionotropic glutamate receptor, metazoa	Family
B, D	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
B, D	IPR001828	Receptor, ligand binding region	Domain

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Other Ion Channels	GluN1a/GluN2B NMDA receptor

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.