SMTL ID : 4nf5.1

Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and D-AP5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: H.272, M.277, E.278, D.281, R.286 Chain B: I.236, F.237, A.238, T.239 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.272, A:D.281, A:R.286, B:A.238, B:T.239 GOL.4: 8 residues within 4Å: Chain B: T.113, T.131, G.132, I.133, S.170, T.171, D.212 Ligands: 2JJ.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.113, B:T.171, B:D.212, B:D.212 GOL.5: 2 residues within 4Å: Chain A: N.274 Chain B: N.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.178 Water bridges: B:Y.179

1 x 2JJ: 5-phosphono-D-norvaline(Non-covalent)

2JJ.3: 11 residues within 4Å: Chain B: H.85, S.111, L.112, T.113, R.118, G.169, S.170, T.171, Y.211, Y.242 Ligands: GOL.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.111, B:T.113, B:S.170, B:T.171 Water bridges: B:E.172 Salt bridges: B:H.85, B:R.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jespersen, A. et al., Structural Insights into Competitive Antagonism in NMDA Receptors. Neuron (2014)

Release Date

2014-03-12

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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