SMTL ID : 5un1.2 (1 other biounit)

Crystal structure of GluN1/GluN2B delta-ATD NMDA receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

hetero-2-2-mer

Ligands

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GLY: GLYCINE(Non-covalent)

GLY.2: 9 residues within 4Å: Chain A: F.89, P.121, L.122, T.123, R.128, S.284, S.285, D.329, F.355 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.123, A:T.123, A:S.285, A:D.329 Salt bridges: A:R.128

2 x GLU: GLUTAMIC ACID(Non-covalent)(Covalent)

GLU.3: 8 residues within 4Å: Chain B: H.84, G.85, S.110, L.111, T.112, R.117, S.278, Y.350 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:H.84, B:L.111 Hydrogen bonds: B:G.85, B:T.112, B:T.112, B:R.117, B:S.278, B:S.278, B:Y.319 Salt bridges: B:H.84, B:R.117 GLU.7: 10 residues within 4Å: Chain D: E.11, H.84, S.110, L.111, T.112, R.117, S.278, Y.319, D.320, Y.350 10 PLIP interactions: 8 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:T.112, D:T.112, D:S.278, D:Y.319, D:D.320, D:Y.350, E.7, E.7 Salt bridges: D:H.84, D:R.117

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.4: 2 residues within 4Å: Chain B: P.275, N.276 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.276 NAG.6: 2 residues within 4Å: Chain C: E.384 Chain D: N.286 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.286, D:N.286 NAG.8: 4 residues within 4Å: Chain D: V.274, P.275, N.276, R.300 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.274 Hydrogen bonds: D:N.276

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

BMK.5: 10 residues within 4Å: Chain A: V.241, A.242 Chain B: N.203, L.231, T.235 Chain C: V.241, A.242, T.245 Chain D: L.231, T.235 7 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: D:T.235, C:V.241, C:A.242, C:T.245, A:V.241, A:V.241, B:T.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, X. et al., Mechanism of NMDA receptor channel block by MK-801 and memantine. Nature (2018)

Release Date

2018-02-07

Peptides

N-methyl-D-aspartate receptor subunit NR1-3a: AC
Ionotropic glutamate receptor subunit NR2B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Membrane

We predict this structure to be a membrane protein.
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N-methyl-D-aspartate receptor subunit NR1-3a

Ionotropic glutamate receptor subunit NR2B

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