SMTL ID : 4tlm.1

Crystal structure of GluN1/GluN2B NMDA receptor, structure 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.77 Å

Oligo State

hetero-2-2-mer

Ligands

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 3 residues within 4Å: Chain A: I.5, N.7, N.40 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.5 Hydrogen bonds: A:N.7, A:N.40 NAG.2: 4 residues within 4Å: Chain A: N.252, N.255, A.258, V.313 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.258, A:V.313 Hydrogen bonds: A:N.255 NAG.3: 1 residues within 4Å: Chain A: N.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.182 NAG.6: 3 residues within 4Å: Chain B: R.313, Y.314, N.317 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.313 Hydrogen bonds: B:N.317 NAG.7: 4 residues within 4Å: Chain C: I.5, N.7, N.40, A.41 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.5 Hydrogen bonds: C:N.7, C:N.40 NAG.8: 4 residues within 4Å: Chain C: H.17, I.20, N.255, S.257 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.17, C:N.255, C:S.257, C:S.257 NAG.10: 3 residues within 4Å: Chain D: I.464, P.651, N.652 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:P.651 Hydrogen bonds: D:N.652

1 x 1AC: 1-AMINOCYCLOPROPANECARBOXYLIC ACID(Non-covalent)

1AC.4: 8 residues within 4Å: Chain A: F.461, L.494, T.495, R.500, S.656, S.657, W.700, D.701 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.461 Hydrogen bonds: A:P.493, A:T.495, A:T.495, A:S.657, A:S.657, A:D.701 Salt bridges: A:R.500

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

QEM.5: 17 residues within 4Å: Chain A: Y.88, T.89, F.92, R.94, K.110, S.111, I.112, L.114 Chain B: A.83, I.87, F.90, T.150, Y.151, F.152, P.153, T.209, E.212 16 PLIP interactions: 6 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:Y.88, A:Y.88, A:F.92, A:L.114, B:A.83, B:I.87, B:I.87, B:F.90, B:F.90, B:F.152, B:F.152, B:P.153 Hydrogen bonds: A:I.112, A:L.114, B:T.150, B:Y.151 QEM.9: 14 residues within 4Å: Chain C: P.85, Y.88, T.89, F.92, K.110, S.111, I.112, H.113, L.114 Chain D: Q.86, I.87, F.90, Y.151, F.152 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:I.87, D:F.90, D:F.90, C:Y.88, C:F.92, C:L.114, C:L.114 Hydrogen bonds: D:Q.86, D:Y.151, C:I.112, C:L.114

1 x JEG: trans-1-aminocyclobutane-1,3-dicarboxylic acid(Non-covalent)

JEG.11: 8 residues within 4Å: Chain D: H.460, S.486, L.487, T.488, G.653, S.654, T.655, D.696 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.488, D:T.488, D:T.488, D:S.654, D:S.654, D:D.696 Salt bridges: D:H.460

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, C.H. et al., NMDA receptor structures reveal subunit arrangement and pore architecture. Nature (2014)

Release Date

2014-07-02

Peptides

receptor subunit GluN1: AC
receptor subunit GluN2B: 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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receptor subunit GluN1

receptor subunit GluN2B

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