SMTL ID : 6whu.1

GluN1b-GluN2B NMDA receptor in complex with SDZ 220-040 and L689,560, class 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 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: 1 residues within 4Å: Chain B: N.573 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain D: N.573 No protein-ligand interaction detected (PLIP)

2 x QGM: (2R,4S)-5,7-dichloro-4-[(phenylcarbamoyl)amino]-1,2,3,4-tetrahydroquinoline-2-carboxylic acid(Non-covalent)

QGM.3: 12 residues within 4Å: Chain A: Q.426, F.505, P.537, L.538, T.539, R.544, Q.707, S.708, S.709, W.752, D.753, V.756 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.537, A:D.753 Hydrogen bonds: A:P.537, A:T.539, A:S.709 Salt bridges: A:R.544 QGM.9: 12 residues within 4Å: Chain C: Q.426, F.505, P.537, L.538, T.539, R.544, Q.707, S.708, S.709, W.752, D.753, V.756 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:P.537, C:D.753 Hydrogen bonds: C:P.537, C:T.539, C:S.709 Salt bridges: C:R.544

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 1 residues within 4Å: Chain A: N.297 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: N.224, T.226 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain B: N.105 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain B: N.719 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.719 NAG.10: 1 residues within 4Å: Chain C: N.297 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain C: N.224, T.226 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain D: N.105 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain D: N.719 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.719

2 x QGP: (2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid(Non-covalent)

QGP.6: 14 residues within 4Å: Chain B: E.444, A.445, P.446, H.517, S.543, L.544, T.545, R.550, G.720, S.721, T.722, Y.762, V.766, Y.793 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.766 Hydrogen bonds: B:H.517, B:T.545, B:T.545, B:S.721, B:S.721, B:T.722 Salt bridges: B:H.517, B:R.550 Halogen bonds: B:Y.793 QGP.12: 14 residues within 4Å: Chain D: E.444, A.445, P.446, H.517, S.543, L.544, T.545, R.550, G.720, S.721, T.722, Y.762, V.766, Y.793 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:V.766 Hydrogen bonds: D:H.517, D:T.545, D:T.545, D:S.721, D:S.721, D:T.722 Salt bridges: D:H.517, D:R.550 Halogen bonds: D:Y.793

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chou, T.H. et al., Structural Basis of Functional Transitions in Mammalian NMDA Receptors. Cell (2020)

Release Date

2020-08-05

Peptides

Glutamate receptor ionotropic, NMDA 1: AC
Glutamate receptor ionotropic, NMDA 2B: 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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Glutamate receptor ionotropic, NMDA 1

Glutamate receptor ionotropic, NMDA 2B

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