SMTL ID : 6e7t.1 (1 other biounit)

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 3 residues within 4Å: Chain A: Q.349, N.367, Y.370 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: N.275, S.277, A.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.275, A:A.278 NAG.7: 1 residues within 4Å: Chain B: N.43 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.43 NAG.8: 1 residues within 4Å: Chain B: N.310 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: Y.106, F.115, D.342 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.115 Water bridges: A:F.115

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: C.57, G.306, C.307, V.308 Chain B: K.48 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: V.363, Q.373, N.374, R.376 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: N.28, K.29, H.31, T.33 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: I.102, Q.122, S.229, L.230 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: M.42, N.43, E.44 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: F.83, A.86, Q.87, D.107 Ligand excluded by PLIP

1 x HYY: N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide(Non-covalent)

HYY.12: 20 residues within 4Å: Chain A: Y.87, T.88, F.91, K.109, S.110, I.111, L.113 Chain B: P.47, Q.79, I.80, F.83, D.105, T.143, Y.144, F.145, P.146, L.174, M.176, S.177, E.205 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:Q.79, B:F.83, B:F.145, A:Y.87, A:Y.87, A:I.111, A:L.113, A:L.113 Hydrogen bonds: B:Q.79, B:T.143, B:Y.144, B:M.176, B:S.177 Water bridges: A:R.93, A:R.93 pi-Cation interactions: A:Y.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Regan, M.C. et al., Structural elements of a pH-sensitive inhibitor binding site in NMDA receptors. Nat Commun (2019)

Release Date

2019-01-30

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, NMDA 1

Glutamate receptor ionotropic, NMDA 2B

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