6MMM | pdb_00006mmm

Diheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-1' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
DSCOP2B SuperfamilyType 2 solute binding protein-like 8036603 3000083 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyType 2 solute binding protein-like 8036603 3000083 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyType 2 solute binding protein-like 8036603 3000083 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyType 2 solute binding protein-like 8036603 3000083 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyType 2 solute binding protein-like 8034027 3000083 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyType 2 solute binding protein-like 8034027 3000083 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
DLig_chane6mmmD4 A: alpha complex topologyX: Voltage-gated ion channels (From Topology)H: Voltage-gated ion channels (From Topology)T: Voltage-gated ion channelsF: Lig_chanECOD (1.6)
DANF_receptor_3rde6mmmD5 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_2nde6mmmD2 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: Periplasmic binding protein-like IF: ANF_receptor_2ndECOD (1.6)
DLig_chan_1e6mmmD1 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)
DLig_chan_5e6mmmD3 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)
BLig_chane6mmmB5 A: alpha complex topologyX: Voltage-gated ion channels (From Topology)H: Voltage-gated ion channels (From Topology)T: Voltage-gated ion channelsF: Lig_chanECOD (1.6)
BANF_receptor_3rde6mmmB2 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_2nde6mmmB1 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_1e6mmmB3 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)
BLig_chan_5e6mmmB4 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)
CLig_chane6mmmC3 A: alpha complex topologyX: Voltage-gated ion channels (From Topology)H: Voltage-gated ion channels (From Topology)T: Voltage-gated ion channelsF: Lig_chanECOD (1.6)
CANF_receptor_3rde6mmmC5 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_2nde6mmmC1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: Periplasmic binding protein-like IF: ANF_receptor_2ndECOD (1.6)
CSBP_bac_3_1ste6mmmC2 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_1e6mmmC4 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)
ALig_chane6mmmA5 A: alpha complex topologyX: Voltage-gated ion channels (From Topology)H: Voltage-gated ion channels (From Topology)T: Voltage-gated ion channelsF: Lig_chanECOD (1.6)
AANF_receptor_3rde6mmmA2 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_2nde6mmmA3 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: Periplasmic binding protein-like IF: ANF_receptor_2ndECOD (1.6)
ASBP_bac_3_1ste6mmmA1 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_1e6mmmA4 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
PF00060Ligand-gated ion channel (Lig_chan)Ligand-gated ion channel- Family
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
PF00060Ligand-gated ion channel (Lig_chan)Ligand-gated ion channel- Family
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
Glutamate receptor ionotropic, NMDA 2A
A, C
Glutamate receptor ionotropic, NMDA 1

InterPro: Protein Family Classification InterPro Database Homepage

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

Membrane Protein Annotation: OPM OPM Database Homepage

ChainsExternal LinkTypeClassSuperfamilyFamily
A, B, C, D
OPMTransmembraneAlpha-helical polytopicIon channel (VIC) superfamilyGlutamate-gated Ion Channel (GIC) family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

ChainsExternal LinkComment
A, B, C, D
PDBTMAnnotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

ChainsExternal LinkComment
A, B, C, D
MemProtMDAnnotated as membrane protein by MemProtMD