SMTL ID : 5un1.1 (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 GLY: GLYCINE(Covalent)

GLY.1: 9 residues within 4Å: Chain A: F.89, P.121, L.122, T.123, R.128, S.285, W.328, D.329, F.355 7 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain A Hydrogen bonds: G.1, A:P.121, A:P.121, A:T.123, A:S.285, A:S.285 Salt bridges: A:R.128

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

NAG.2: 4 residues within 4Å: Chain A: E.74, N.372, K.375 Chain B: E.119 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.74, B:E.119 NAG.8: 2 residues within 4Å: Chain B: P.275, N.276 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.276 NAG.10: 3 residues within 4Å: Chain D: P.275, N.276, R.300 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.275, D:N.276

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 3 residues within 4Å: Chain A: D.274, I.277, K.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.274, A:K.305

3 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 6 residues within 4Å: Chain A: Y.17, E.30, I.33, Y.61, T.388, W.389 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:W.389 Hydrogen bonds: A:I.33, A:T.388, E.4, E.4 Salt bridges: A:R.19 GLU.6: 4 residues within 4Å: Chain A: R.352 Chain B: I.128, E.129, L.385 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:R.352, A:R.352 GLU.7: 9 residues within 4Å: Chain B: H.84, S.110, L.111, T.112, R.117, G.277, S.278, D.320, Y.350 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:T.112, B:T.112, B:S.278, B:S.278, B:S.278, E.7, E.7 Salt bridges: B:H.84, B:R.117

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

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

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.9: 1 residues within 4Å: Chain C: R.28 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.28

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
G

C
E

B
H

D
F

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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