SMTL ID : 7f5b.1

LBD-TMD focused reconstruction of DNQX-bound GluK2-1xNeto2 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 5 residues within 4Å: Chain B: R.543, N.546, T.548, T.730 Ligands: NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 6 residues within 4Å: Chain D: R.543, N.546, T.548, T.730, S.731 Ligands: NAG.9 No protein-ligand interaction detected (PLIP)

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

NAG.3: 6 residues within 4Å: Chain A: R.543, L.729, N.749, N.751, E.808 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.749 NAG.4: 3 residues within 4Å: Chain A: R.543, N.546 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.543 NAG.6: 4 residues within 4Å: Chain B: C.750, N.751 Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.751 NAG.7: 5 residues within 4Å: Chain C: R.543, N.546, N.549, L.729 Ligands: NAG.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.543, C:N.549, C:L.729 NAG.8: 4 residues within 4Å: Chain C: R.543, C.750, N.751 Ligands: NAG.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.543, C:R.543 NAG.9: 4 residues within 4Å: Chain D: L.729, N.749, N.751 Ligands: NAG-NAG-BMA.2 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.751

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain A: Q.621 Chain B: Q.621 Chain D: Q.621 No protein-ligand interaction detected (PLIP)

1 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.10: 4 residues within 4Å: Chain C: Y.566, A.570 Chain D: F.824, I.825 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.824, D:I.825, C:Y.566, C:A.570

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, L. et al., Kainate receptor modulation by NETO2. Nature (2021)

Release Date

2021-09-29

Peptides

Glutamate receptor ionotropic, kainate 2: ABCD
Neuropilin and tolloid-like protein 2: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor ionotropic, kainate 2

Neuropilin and tolloid-like protein 2

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