SMTL ID : 5h8f.1

Structure of the apo human GluN1/GluN2A LBD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

hetero-1-1-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: I.238, F.239, A.240, T.241 Chain B: H.273, E.279 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:A.240, A:T.241, B:H.273, B:E.279 Water bridges: B:E.279, B:E.279, B:D.282 GOL.3: 3 residues within 4Å: Chain B: T.28, C.29, K.42 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.29, B:C.29, B:K.42 Water bridges: B:K.42, B:I.44 GOL.4: 6 residues within 4Å: Chain B: F.33, T.34, V.35, T.284, W.285, Y.288 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.35, B:T.284 GOL.5: 7 residues within 4Å: Chain B: T.34, D.38, P.39, V.40, K.41, D.70, W.285 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.41, B:D.70 Water bridges: B:K.41, B:K.41, B:D.70, B:T.284 GOL.6: 6 residues within 4Å: Chain B: D.120, R.256, D.258, S.259, P.260, W.261 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.120, B:R.256, B:D.258 Water bridges: B:S.259 GOL.7: 6 residues within 4Å: Chain A: D.259 Chain B: A.133, I.136, E.137, F.138, K.257 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.136, B:F.138, B:K.257, A:D.259 Water bridges: A:R.256

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 10 residues within 4Å: Chain A: H.87, S.113, L.114, T.115, R.120, G.171, S.172, T.173, Y.213, D.214 13 PLIP interactions: 9 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:Y.213 Hydrogen bonds: A:T.115, A:T.115, A:S.172, A:T.173, A:D.214, E.2, E.2, E.2, E.2 Water bridges: A:E.174 Salt bridges: A:H.87, A:R.120

1 x GLY: GLYCINE(Non-covalent)

GLY.8: 10 residues within 4Å: Chain B: F.93, P.125, L.126, T.127, R.132, S.180, S.181, W.224, D.225, F.251 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:P.125, B:T.127, B:S.181, B:S.181, B:D.225, G.8 Salt bridges: B:R.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hackos, D.H. et al., Positive Allosteric Modulators of GluN2A-Containing NMDARs with Distinct Modes of Action and Impacts on Circuit Function. Neuron (2016)

Release Date

2016-02-24

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, NMDA 2A

Glutamate receptor ionotropic, NMDA 1

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