SMTL ID : 5iov.1

Cryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/glycine/Ro25-6981-bound conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 7.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GLY: GLYCINE(Non-covalent)

GLY.1: 4 residues within 4Å: Chain A: P.492, L.493, T.494, S.656 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.492, A:T.494 GLY.2: 4 residues within 4Å: Chain B: P.492, L.493, T.494, S.656 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.492, B:T.494

2 x QEM: 4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol(Non-covalent)

QEM.3: 8 residues within 4Å: Chain A: P.84, Y.87, T.88 Chain C: A.102, Q.105, F.109, Y.170, F.171 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.87, C:Q.105, C:F.109 Hydrogen bonds: C:Y.170 QEM.5: 9 residues within 4Å: Chain B: Y.87, S.110, L.113 Chain D: A.102, Q.105, I.106, F.109, Y.170, F.171 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:A.102, D:I.106, D:F.109, B:Y.87 Hydrogen bonds: D:Y.170

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 4 residues within 4Å: Chain C: S.505, G.672, S.673, D.715 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:D.715 Hydrogen bonds: C:S.673, C:D.715, E.4, E.4 GLU.6: 4 residues within 4Å: Chain D: S.505, G.672, S.673, T.674 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain D Hydrogen bonds: E.6, E.6, D:S.673, D:T.674

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, S. et al., Mechanism of NMDA Receptor Inhibition and Activation. Cell (2016)

Release Date

2016-04-20

Peptides

N-methyl-D-aspartate receptor subunit NR1-8a: AB
Ionotropic glutamate receptor subunit NR2B: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

Membrane

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

Ionotropic glutamate receptor subunit NR2B

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