SMTL ID : 5vii.1

Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-(3-fluoropropyl)phenyl-ACEPC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLY: GLYCINE(Non-covalent)

GLY.1: 10 residues within 4Å: Chain A: F.92, P.124, L.125, T.126, R.131, S.179, S.180, W.223, D.224, F.250 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:P.124, A:T.126, A:S.180, A:S.180, A:D.224, G.1 Salt bridges: A:R.131

1 x 5DY: 5-[(2R)-2-amino-2-carboxyethyl]-1-[4-(3-fluoropropyl)phenyl]-1H-pyrazole-3-carboxylic acid(Non-covalent)

5DY.2: 20 residues within 4Å: Chain A: E.273 Chain B: H.85, S.111, L.112, T.113, I.114, N.115, R.118, G.132, I.133, G.169, S.170, T.171, N.174, Y.211, D.212, A.238, T.240, Y.242 Ligands: TRS.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.113, B:I.133, B:A.238, B:T.240 Hydrogen bonds: B:S.111, B:T.113, B:S.170, B:S.170, B:T.171, B:Y.211, B:D.212 Water bridges: B:G.169, B:S.170, B:S.170 Salt bridges: B:H.85, B:R.118 Halogen bonds: B:I.114

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: E.273, N.274 Chain B: R.173, N.174, N.177, N.178 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.173, B:R.173, B:N.177 Water bridges: B:N.174, B:N.177, A:E.273

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

TRS.4: 10 residues within 4Å: Chain B: K.84, H.85, G.86, K.87, N.94, R.118, N.168, G.169, S.170 Ligands: 5DY.2 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.84, B:H.85, B:G.86, B:G.86, B:N.94, B:R.118 Water bridges: B:S.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lind, G.E. et al., Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-04-26

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, NMDA 1

Glutamate receptor ionotropic, NMDA 2A

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