5IPU | pdb_00005ipu

Cryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV-bound conformation, state 6

External Resource: Annotation


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
DANF_receptor_3rde5ipuD3 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: Periplasmic binding protein-like IF: ANF_receptor_3rdECOD (1.6)
DANF_receptor_2nde5ipuD1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: Periplasmic binding protein-like IF: ANF_receptor_2ndECOD (1.6)
DSBP_bac_3_1ste5ipuD2 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_3_1stECOD (1.6)
DLig_chan_5e5ipuD4 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: Lig_chan_5ECOD (1.6)
BANF_receptor_3rde5ipuB2 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: Periplasmic binding protein-like IF: ANF_receptor_3rdECOD (1.6)
BANF_receptor_2nde5ipuB1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: Periplasmic binding protein-like IF: ANF_receptor_2ndECOD (1.6)
BLig_chan_5e5ipuB3 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: Lig_chan_5ECOD (1.6)
CANF_receptor_3rde5ipuC5 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: Periplasmic binding protein-like IF: ANF_receptor_3rdECOD (1.6)
CANF_receptor_2nd,ANF_receptor_1ste5ipuC3 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: Periplasmic binding protein-like IF: ANF_receptor_2nd,ANF_receptor_1stECOD (1.6)
CSBP_bac_3_1ste5ipuC4 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_3_1stECOD (1.6)
CLig_chan_1e5ipuC2 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: Lig_chan_1ECOD (1.6)
AANF_receptor_3rde5ipuA5 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: Periplasmic binding protein-like IF: ANF_receptor_3rdECOD (1.6)
AANF_receptor_2nd,ANF_receptor_1ste5ipuA4 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: Periplasmic binding protein-like IF: ANF_receptor_2nd,ANF_receptor_1stECOD (1.6)
ASBP_bac_3_1ste5ipuA2 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: SBP_bac_3_1stECOD (1.6)
ALig_chan_1e5ipuA3 A: a/b three-layered sandwichesX: Periplasmic binding protein-like II (From Topology)H: Periplasmic binding protein-like II (From Topology)T: Periplasmic binding protein-like IIF: Lig_chan_1ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
B, D
PF01094Receptor family ligand binding region (ANF_receptor)Receptor family ligand binding regionThis family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure. Domain
B, D
PF10613Ligated ion channel L-glutamate- and glycine-binding site (Lig_chan-Glu_bd)Ligated ion channel L-glutamate- and glycine-binding siteThis 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
A, C
PF01094Receptor family ligand binding region (ANF_receptor)Receptor family ligand binding regionThis family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure. Domain
A, C
PF10613Ligated ion channel L-glutamate- and glycine-binding site (Lig_chan-Glu_bd)Ligated ion channel L-glutamate- and glycine-binding siteThis 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B, D
Ionotropic glutamate receptor subunit NR2B
A, C
N-methyl-D-aspartate receptor subunit NR1-8a

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
B, D
IPR028082Periplasmic binding protein-like IHomologous Superfamily
B, D
IPR018884Glutamate [NMDA] receptor, epsilon subunit, C-terminalDomain
B, D
IPR019594Ionotropic glutamate receptor, L-glutamate and glycine-binding domainDomain
B, D
IPR015683Ionotropic glutamate receptorFamily
B, D
IPR001508Ionotropic glutamate receptor, metazoaFamily
B, D
IPR001320Ionotropic glutamate receptor, C-terminalDomain
B, D
IPR001828Receptor, ligand binding regionDomain
A, C
IPR001320Ionotropic glutamate receptor, C-terminalDomain
A, C
IPR028082Periplasmic binding protein-like IHomologous Superfamily
A, C
IPR049873Glutamate [NMDA] receptor subunit 1-like, N-terminal LIVBP-like domainDomain
A, C
IPR019594Ionotropic glutamate receptor, L-glutamate and glycine-binding domainDomain
A, C
IPR015683Ionotropic glutamate receptorFamily
A, C
IPR049872Glutamate [NMDA] receptor subunit 1-like, ligand-binding domainDomain
A, C
IPR001508Ionotropic glutamate receptor, metazoaFamily
A, C
IPR001828Receptor, ligand binding regionDomain

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

ChainsResource LinkGroupSubgroupProtein
A, B, C, D
mpstrucTRANSMEMBRANE PROTEINS: ALPHA-HELICALChannels: Other Ion ChannelsGluN1a/GluN2B NMDA receptor