SMTL ID : 5uow.1

Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with glycine, glutamate, MK-801 and a GluN2B-specific Fab, at pH 6.5

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.50 Å

Oligo State

hetero-2-1-1-2-mer

Ligands

8 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: 4 residues within 4Å: Chain A: I.4, N.39, A.40, T.41 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.181 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.254 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: N.6, N.39, A.40, T.41 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain C: N.181 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.254, S.256, A.257 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain D: N.336 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain D: N.681 No protein-ligand interaction detected (PLIP)

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.9: 7 residues within 4Å: Chain B: H.473, S.499, T.501, G.676, S.677, T.678, D.719 8 PLIP interactions: 5 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: B:T.501, B:T.501, B:S.677, B:T.678, E.9, E.9, E.9 Salt bridges: B:H.473

1 x BMK: (5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene(Non-covalent)

BMK.10: 8 residues within 4Å: Chain B: L.630, A.631, T.634 Chain C: T.624, L.627 Chain D: L.636, A.637, T.640 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: C:T.624, C:L.627, B:L.630, B:T.634, D:L.636

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, W. et al., Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation. Science (2017)

Release Date

2017-03-22

Peptides

N-methyl-D-aspartate receptor subunit NR1-8a: AC
N-methyl-D-aspartate receptor subunit NR2A: B
Ionotropic glutamate receptor subunit NR2B: D
GluN2B-specific Fab, termed 11D1: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
F

F
G

Membrane

We predict this structure to be a membrane protein.
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N-methyl-D-aspartate receptor subunit NR1-8a

N-methyl-D-aspartate receptor subunit NR2A

Ionotropic glutamate receptor subunit NR2B

GluN2B-specific Fab, termed 11D1

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