SMTL ID : 8jj0.1

Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab5F6 in one fab bind 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: 6 residues within 4Å: Chain D: N.28, N.61, A.62, T.63, S.64, S.85 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.64, D:S.64

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

NAG.2: 5 residues within 4Å: Chain B: I.26, R.43, N.61, A.62, T.63 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.26 Hydrogen bonds: B:R.43, B:N.61 NAG.3: 2 residues within 4Å: Chain B: K.202, N.203 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.203 NAG.4: 1 residues within 4Å: Chain B: N.471 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain B: W.768, N.771 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.768 Hydrogen bonds: B:N.771 NAG.6: 4 residues within 4Å: Chain C: K.487, P.686, N.687, R.695 No protein-ligand interaction detected (PLIP) NAG.7: 6 residues within 4Å: Chain D: N.276, S.278, A.279, V.334 Chain E: Y.52, K.76 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:K.76, E:K.76, D:N.276, D:A.279 NAG.8: 1 residues within 4Å: Chain D: N.471 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.471 NAG.9: 4 residues within 4Å: Chain D: W.768, Q.770, N.771, L.774 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.774

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
Fab5F6 Heavy Chain: E
Fab5F6 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

Fab5F6 Heavy Chain

Fab5F6 Light Chain

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