SMTL ID : 9c7c.1

Diheteromeric GluN1/GluN2A (delM653) in nanodisc complexed with glycine, glutamate, and GNE-4123, open conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

11 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: I.26, N.28, N.61, A.62, T.63 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.368, G.369, H.371, I.373 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: M.394, P.767, W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.380 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.686, R.710 Ligands: NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: N.28, N.61, A.62, S.85 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain C: N.203 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: N.368, T.370, H.371, I.373 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.371 NAG-NAG.9: 2 residues within 4Å: Chain C: T.396, N.471 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: P.767, W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain D: V.489, P.685, N.686, R.710 Ligands: NAG.48 No protein-ligand interaction detected (PLIP)

2 x 01: 4-cyclohexyl-N-[(8R)-2-cyclopropyl-7-hydroxy-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]benzene-1-sulfonamide

01.12: 3 residues within 4Å: Chain A: L.551, D.552, F.554 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.551, A:D.552, A:F.554 Hydrogen bonds: A:L.551, A:D.552 01.34: 5 residues within 4Å: Chain C: S.549, L.551, D.552, M.818, L.819 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:D.552, C:M.818 Hydrogen bonds: C:L.551, C:D.552, C:D.552

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

NAG.13: 2 residues within 4Å: Chain A: N.203, T.205 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: R.212, L.238, N.239 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.273, N.276, V.334 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: T.335, F.348, N.350 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.440, D.441, P.447, H.449 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: T.396, N.471 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.491 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: H.42, N.75 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.340 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: I.442, N.443, T.446, E.448 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.444 Ligands: NAG-NAG.5 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.541 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: R.212, M.237, L.238, N.239 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.276, A.279, V.334 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: E.299, N.300 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: T.335, F.348, N.350 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.440, D.441, H.449 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.491 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain D: N.75 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain D: N.340 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain D: N.380, T.382 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: N.443, S.445 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain D: N.444, N.447 Ligands: NAG-NAG.11 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain D: N.541 Ligand excluded by PLIP

1 x HP6: HEPTANE(Non-covalent)

HP6.20: 6 residues within 4Å: Chain A: W.563, W.611, L.614, L.615 Chain D: F.636 Ligands: Y01.21 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.611, A:L.615, D:F.636

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.21: 11 residues within 4Å: Chain A: H.571, S.604, M.607, W.608, W.611, E.834, Y.837 Chain D: T.625, I.629 Ligands: HP6.20, HEX.53 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:M.607, A:W.608, D:T.625, D:I.629 Y01.28: 9 residues within 4Å: Chain A: V.635 Chain B: P.546, S.547, L.550, M.822, A.825, A.826, L.829 Ligands: Y01.29 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.635, B:P.546, B:L.550, B:M.822, B:A.825, B:A.826, B:L.829 Y01.29: 9 residues within 4Å: Chain B: S.547, L.550, A.555, W.558, F.562, V.563, I.567, W.609 Ligands: Y01.28 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.555, B:W.558, B:F.562, B:V.563, B:I.567 Hydrogen bonds: B:S.547 Y01.31: 7 residues within 4Å: Chain A: L.565 Chain B: I.813, D.814, F.820, Y.821, A.824, M.827 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.813, B:F.820, B:A.824, A:L.565, A:L.565 Y01.42: 10 residues within 4Å: Chain B: I.629 Chain C: H.571, L.603, S.604, M.607, W.608, W.611, Y.837 Ligands: D10.33, D10.41 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.608, C:W.611, C:Y.837 Hydrogen bonds: C:Y.837, C:Y.837 Y01.50: 8 residues within 4Å: Chain C: V.635 Chain D: P.546, S.547, M.822, A.825, L.829 Ligands: Y01.51, D12.52 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.546, D:A.825, D:L.829, C:V.635 Y01.51: 8 residues within 4Å: Chain D: S.547, L.550, A.555, W.558, F.562, I.567 Ligands: Y01.50, D12.52 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.555, D:W.558, D:W.558, D:F.562, D:F.562, D:I.567 Hydrogen bonds: D:S.547, D:S.547 Y01.54: 8 residues within 4Å: Chain C: L.565 Chain D: I.813, D.814, A.817, F.820, Y.821, A.824, M.827 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.565, C:L.565, D:I.813, D:Y.821

2 x GLY: GLYCINE(Non-covalent)

GLY.22: 9 residues within 4Å: Chain A: F.484, P.516, L.517, T.518, R.523, S.688, W.731, D.732, F.758 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.516, A:T.518, A:S.688, A:S.688 Salt bridges: A:R.523 GLY.43: 10 residues within 4Å: Chain C: F.484, P.516, L.517, T.518, R.523, S.687, S.688, W.731, D.732, F.758 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.516, C:T.518, C:S.688 Salt bridges: C:R.523

2 x D12: DODECANE(Non-covalent)

D12.30: 5 residues within 4Å: Chain A: M.634, V.635 Chain B: W.558, I.605, W.609 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.558, B:I.605, B:W.609, B:W.609, A:M.634, A:V.635 D12.52: 8 residues within 4Å: Chain C: R.630, I.631, M.634, V.635 Chain D: I.605, W.609 Ligands: Y01.50, Y01.51 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.605, D:W.609, D:W.609, C:I.631, C:V.635

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.32: 11 residues within 4Å: Chain B: H.485, S.511, T.513, R.518, V.684, G.687, S.688, T.689, Y.729, D.730, Y.760 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:S.511, B:T.513, B:T.513, B:S.688, B:T.689, B:D.730, B:D.730, E.32 Salt bridges: B:H.485, B:R.518 GLU.55: 10 residues within 4Å: Chain D: H.485, S.511, T.513, R.518, G.687, S.688, T.689, Y.729, D.730, Y.760 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:Y.729 Hydrogen bonds: D:S.511, D:T.513, D:T.513, D:S.688, D:T.689, D:D.730 Salt bridges: D:H.485, D:R.518

2 x D10: DECANE(Non-covalent)

D10.33: 7 residues within 4Å: Chain B: I.629, S.632, F.636 Chain C: W.611, L.819 Ligands: D10.41, Y01.42 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.611, C:W.611, C:L.819, B:I.629, B:F.636 D10.41: 6 residues within 4Å: Chain C: M.555, S.560, W.563, G.567 Ligands: D10.33, Y01.42 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.563

1 x HEX: HEXANE(Non-covalent)

HEX.53: 5 residues within 4Å: Chain A: W.611 Chain D: I.629, S.632, F.636 Ligands: Y01.21 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.629, D:F.636, A:W.611

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jalali-Yazdi, F. et al., Diheteromeric GluN1/GluN2A (delM563) in nanodisc, in complex with glycine, glutamate, and GNE-4123, open-pore conformation. To Be Published

Release Date

2025-09-24

Peptides

Glutamate receptor ionotropic, NMDA 1,Green fluorescent protein: AC
Glutamate receptor ionotropic, NMDA 2A,Green fluorescent protein chimera: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Glutamate receptor ionotropic, NMDA 1,Green fluorescent protein

Glutamate receptor ionotropic, NMDA 2A,Green fluorescent protein chimera

Related Entries With Identical Sequence