SMTL ID : 6e7r.2 (1 other biounit)

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 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: 4 residues within 4Å: Chain A: N.367, S.369, Y.370, I.372 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: N.275, A.278, V.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.275, A:A.278 NAG.6: 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:D.342 Water bridges: A:F.115

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

CL.4: 4 residues within 4Å: Chain A: C.57, G.306, C.307, V.308 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: H.72, R.102, M.103 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: M.101, I.102, Q.122, S.229, L.230 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: M.42, N.43, E.44 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: Y.357, Y.358, V.359 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: E.75, E.204 Ligand excluded by PLIP

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

HYS.7: 19 residues within 4Å: Chain A: Y.87, T.88, F.91, S.110, I.111, L.113 Chain B: P.47, Q.79, I.80, F.83, T.143, Y.144, F.145, P.146, L.174, D.175, M.176, S.177, E.205 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Q.79, B:F.83, B:F.145, A:Y.87, A:Y.87, A:L.113 Hydrogen bonds: B:T.143, B:T.143, B:Y.144, B:M.176, B:E.205, A:I.111 Water bridges: B:Q.79, A:R.93

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
C

B
D

Glutamate receptor ionotropic, NMDA 1

Glutamate receptor ionotropic, NMDA 2B

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