SMTL ID : 5jty.1

Glutamate- and DCKA-bound GluN1/GluN2A agonist binding domains with MPX-007

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 2JK: 4-hydroxy-5,7-dimethylquinoline-2-carboxylic acid(Non-covalent)

2JK.1: 11 residues within 4Å: Chain A: Q.13, F.16, F.92, P.124, L.125, T.126, R.131, W.223, D.224, V.227, F.250 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.13, A:F.16, A:W.223, A:V.227, A:F.250, A:F.250 Hydrogen bonds: A:P.124, A:T.126 Water bridges: A:T.126 Salt bridges: A:R.131 pi-Stacking: A:F.92

1 x 6ND: 5-({[(3,4-difluorophenyl)sulfonyl]amino}methyl)-6-methyl-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide(Non-covalent)

6ND.2: 16 residues within 4Å: Chain A: I.127, P.140, Y.143, R.247, S.248, G.249 Chain B: V.126, P.127, F.128, V.129, E.130, L.261, V.264, M.269, E.273, L.277 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:R.247, B:V.126, B:V.129, B:V.264, B:L.277 Hydrogen bonds: A:I.127, A:G.249, B:F.128, B:E.130 pi-Stacking: A:Y.143

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.3: 10 residues within 4Å: Chain B: H.85, S.111, L.112, T.113, R.118, G.169, S.170, T.171, Y.211, D.212 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.211 Hydrogen bonds: B:T.113, B:T.113, B:S.170, B:S.170, B:T.171, B:D.212, E.3 Water bridges: B:V.166, B:G.169, B:G.169 Salt bridges: B:H.85, B:R.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yi, F. et al., Structural Basis for Negative Allosteric Modulation of GluN2A-Containing NMDA Receptors. Neuron (2016)

Release Date

2016-09-21

Peptides

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

Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A

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