SMTL ID : 8jj2.1

Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab2G7 in one fab conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain D: I.26, N.61, A.62, T.63, S.85 No protein-ligand interaction detected (PLIP)

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 3 residues within 4Å: Chain A: K.487, N.687, K.711 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.487, A:N.687 NAG.3: 4 residues within 4Å: Chain B: N.61, A.62, T.63, S.85 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain B: N.273, N.276, S.278 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.273, B:S.278, B:S.278 NAG.5: 2 residues within 4Å: Chain B: T.396, N.471 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.471 NAG.6: 2 residues within 4Å: Chain B: M.470, N.771 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain D: N.273, N.276, S.278 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.273, D:S.278, D:S.278 NAG.8: 4 residues within 4Å: Chain D: N.368, G.369, T.370, I.373 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.368, D:G.369 NAG.9: 2 residues within 4Å: Chain D: W.768, N.771 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.768 Hydrogen bonds: D:N.771

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Structural basis for antibody-mediated NMDA receptor clustering and endocytosis in autoimmune encephalitis. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-06-05

Peptides

Glutamate receptor ionotropic, NMDA 2A: AC
Glutamate receptor ionotropic, NMDA 1: BD
Fab2G7 Heavy Chain: E
Fab2G7 Light Chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor ionotropic, NMDA 2A

Glutamate receptor ionotropic, NMDA 1

Fab2G7 Heavy Chain

Fab2G7 Light Chain

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