SMTL ID : 9b37.1

Open state of kainate receptor GluK2 in complex with agonist glutamate and positive allosteric modulator BPAM344 bound to one concanavalin A dimer. Composite map.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: P.545, N.546 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.67, R.68, T.69, L.70, Q.288 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: S.409, N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.275 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: H.34, N.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.73 NAG-NAG.11: 2 residues within 4Å: Chain B: N.67, Q.288 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: N.412, E.415 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: T.33, P.72, N.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.73 NAG-NAG.15: 1 residues within 4Å: Chain C: N.546 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: R.543, R.748, N.749, N.751 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: N.67, Q.288 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain C: N.73 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain D: R.543, N.546, N.749, N.751 Ligands: NAG-NAG-BMA-BMA.21 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain D: N.412 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain D: P.72, N.73 No protein-ligand interaction detected (PLIP)

3 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.2: 3 residues within 4Å: Chain A: R.543, N.749, N.751 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 2 residues within 4Å: Chain C: N.412, E.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 3 residues within 4Å: Chain D: N.67, L.70, Q.288 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.3: 11 residues within 4Å: Chain A: R.158, D.162, R.194, N.378, T.380, N.381, T.385, P.407, A.408, S.409, G.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.409, A:R.158, A:R.158, A:R.194 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.17: 12 residues within 4Å: Chain C: R.158, D.162, R.194, Y.195, N.378, T.380, N.381, A.408, S.409, G.410 Chain D: E.217, R.220 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:R.158 Hydrogen bonds: C:D.162, C:R.158, C:R.158, D:R.220, C:R.194, C:R.194, C:R.194, C:Y.195, C:Y.195

2 x NAG- NAG- BMA- MAN- NAG- GAL- MAN: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-MAN.8: 13 residues within 4Å: Chain B: R.543, N.546, L.729, T.730, S.731, D.732 Chain F: Y.12, G.98, Y.100, T.226, G.227, R.228 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN.9 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:Y.100, F:Y.100, F:Y.100, B:T.730, F:T.226, F:R.228, F:R.228 NAG-NAG-BMA-MAN-NAG-GAL-MAN.9: 4 residues within 4Å: Chain B: R.543, N.751 Chain F: N.237 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN.8 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.237, F:N.237

1 x MAN- NAG- BMA- MAN- NAG- NAG: Cyclic 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)]alpha-D-mannopyranose

MAN-NAG-BMA-MAN-NAG-NAG.10: 7 residues within 4Å: Chain E: Y.12, D.16, G.98, L.99, Y.100, R.228 Ligands: NAG.43 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Y.12, E:Y.12, E:Y.12, E:R.228

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.13: 3 residues within 4Å: Chain B: G.273, N.275, K.395 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.26: 5 residues within 4Å: Chain D: G.273, V.274, N.275, L.394, K.395 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.21: 6 residues within 4Å: Chain D: R.543, N.546, L.729, T.730 Ligands: NAG-NAG.22, NAG-NAG.22 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-MAN-NAG.23: 5 residues within 4Å: Chain C: D.207 Chain D: N.378, K.379, T.380, T.385 No protein-ligand interaction detected (PLIP)

4 x 2J9: 4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

2J9.28: 13 residues within 4Å: Chain A: K.531, P.532, F.533, L.783, Q.786 Chain D: I.519, P.532, M.534, T.535, S.761, K.762, G.763 Ligands: 2J9.56 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:P.532 Halogen bonds: D:M.534 2J9.39: 14 residues within 4Å: Chain B: K.531, P.532, F.533, M.534, T.535, L.783, Q.786 Chain C: I.519, P.532, M.534, S.761, K.762, G.763 Ligands: 2J9.46 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:T.535, C:P.532 Halogen bonds: C:M.534 2J9.46: 14 residues within 4Å: Chain B: I.519, P.532, M.534, T.535, S.761, K.762, G.763 Chain C: K.531, P.532, F.533, L.783, Q.786, L.791 Ligands: 2J9.39 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:P.532, C:L.791 Halogen bonds: B:M.534 2J9.56: 15 residues within 4Å: Chain A: I.519, P.532, M.534, T.535, S.761, K.762, G.763 Chain D: K.531, P.532, F.533, M.534, T.535, L.783, Q.786 Ligands: 2J9.28 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:P.532, D:T.535 Halogen bonds: A:M.534

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.29: 11 residues within 4Å: Chain A: Y.488, P.516, L.517, A.518, R.523, G.688, A.689, T.690, M.737, E.738, Y.764 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.488 Hydrogen bonds: A:P.516, A:A.518, A:A.689, A:T.690, A:T.690, A:Y.764, A:Y.764, E.29 Salt bridges: A:R.523, A:K.762 GLU.40: 11 residues within 4Å: Chain B: Y.488, P.516, L.517, A.518, R.523, G.688, A.689, T.690, M.737, E.738, Y.764 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.488 Hydrogen bonds: B:A.518, B:A.689, B:T.690, B:T.690, B:E.738, B:Y.764, B:Y.764 Salt bridges: B:R.523, B:K.762 GLU.47: 11 residues within 4Å: Chain C: Y.488, P.516, L.517, A.518, R.523, G.688, A.689, T.690, M.737, E.738, Y.764 11 PLIP interactions: 10 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.488 Hydrogen bonds: C:P.516, C:A.518, C:A.689, C:T.690, C:T.690, C:Y.764, C:Y.764, E.47 Salt bridges: C:R.523, C:K.762 GLU.57: 11 residues within 4Å: Chain D: Y.488, P.516, L.517, A.518, R.523, G.688, A.689, T.690, M.737, E.738, Y.764 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:Y.488 Hydrogen bonds: D:A.518, D:A.689, D:T.690, D:T.690, D:E.738, D:Y.764, D:Y.764 Salt bridges: D:R.523, D:K.762

14 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.30: 14 residues within 4Å: Chain A: N.549, F.553, L.556, P.561, W.564, V.567, L.568, L.619, M.620, I.648, V.826 Chain D: F.642 Ligands: POV.31, POV.32 12 PLIP interactions: 2 interactions with chain D, 10 interactions with chain A Hydrophobic interactions: D:F.642, D:F.642, A:F.553, A:L.556, A:L.556, A:W.564, A:W.564, A:V.567, A:L.568, A:L.619, A:I.648, A:V.826 POV.31: 10 residues within 4Å: Chain A: F.553, I.825, V.826, A.828, A.829, G.830, L.833 Ligands: POV.30, POV.32, CLR.34 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.553, A:F.553, A:I.825, A:V.826, A:A.828, A:A.829, A:L.833 POV.32: 9 residues within 4Å: Chain A: M.565, L.568, L.569, L.572, F.612, V.616 Ligands: POV.30, POV.31, POV.38 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.569, A:L.572, A:F.612, A:V.616 POV.37: 9 residues within 4Å: Chain A: K.870, C.871, Q.872 Chain D: F.579, R.583, L.608, Y.844, K.848 Ligands: CLR.53 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.579, D:L.608, A:K.870 Hydrogen bonds: D:Y.844 POV.38: 12 residues within 4Å: Chain A: C.576, F.579, V.580, R.583, T.607, L.608, L.609, F.612 Chain B: K.870, C.871 Ligands: POV.32, CLR.33 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.579, A:V.580, A:L.608, A:L.609, A:F.612 Salt bridges: A:R.583 POV.41: 9 residues within 4Å: Chain A: G.638, F.642 Chain B: F.553, L.556, W.564, L.568, M.620, I.648 Ligands: POV.42 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.553, B:L.556, B:L.556, B:W.564, B:W.564, B:L.568, B:I.648, A:F.642, A:F.642 POV.42: 9 residues within 4Å: Chain A: I.635, I.639 Chain B: V.552, F.553, V.616, V.826, A.829, L.833 Ligands: POV.41 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.616, B:V.826, B:L.833, B:L.833, A:I.635 POV.45: 8 residues within 4Å: Chain B: F.579, L.608, Y.844, K.848 Chain C: K.870, C.871, Q.872 Ligands: CLR.35 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.579, B:L.608 Hydrogen bonds: B:Y.844 POV.48: 13 residues within 4Å: Chain B: G.638, F.642 Chain C: N.549, G.551, F.553, L.556, P.561, W.564, L.568, M.620, V.826 Ligands: POV.49, POV.50 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.553, C:F.553, C:L.556, C:L.556, C:P.561, C:P.561, C:W.564, C:W.564, C:L.568, C:L.568, C:V.826, B:F.642, B:F.642 Hydrogen bonds: C:F.553 POV.49: 9 residues within 4Å: Chain C: F.553, I.825, V.826, A.829, G.830, L.833 Ligands: POV.48, POV.50, CLR.51 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.553, C:F.553, C:I.825, C:V.826, C:A.829, C:L.833 POV.50: 8 residues within 4Å: Chain C: M.565, L.568, L.572, F.612, V.616 Ligands: POV.48, POV.49, POV.55 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.572, C:F.612, C:V.616 POV.55: 12 residues within 4Å: Chain C: C.576, F.579, V.580, R.583, T.607, L.608, L.609, F.612 Chain D: K.870, C.871 Ligands: CLR.44, POV.50 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.579, C:V.580, C:L.609, C:F.612 Salt bridges: C:R.583 POV.58: 9 residues within 4Å: Chain C: G.638, F.642 Chain D: F.553, L.556, W.564, L.568, M.620, I.648 Ligands: POV.59 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.553, D:L.556, D:L.556, D:W.564, D:W.564, D:L.568, D:I.648, C:F.642 POV.59: 10 residues within 4Å: Chain C: I.635, I.639 Chain D: V.552, F.553, W.613, V.616, V.826, A.829, L.833 Ligands: POV.58 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.613, D:V.616, D:V.826, D:L.833, D:L.833, C:I.635

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.33: 5 residues within 4Å: Chain A: G.840, E.841, Y.844 Chain D: Y.587 Ligands: POV.38 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.587, A:E.841, A:Y.844, A:Y.844 CLR.34: 5 residues within 4Å: Chain A: V.817, F.824, A.828 Chain D: Y.566 Ligands: POV.31 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.566, A:V.817, A:F.824, A:A.828 CLR.35: 6 residues within 4Å: Chain A: Y.587, L.631 Chain B: L.609, E.841, Y.844 Ligands: POV.45 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.609, B:E.841, B:Y.844, A:L.631 CLR.36: 5 residues within 4Å: Chain A: Y.566, L.569 Chain B: V.817, F.824, I.825 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.824, B:I.825, A:Y.566 CLR.44: 5 residues within 4Å: Chain B: Y.587 Chain C: G.840, E.841, Y.844 Ligands: POV.55 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:E.841, C:Y.844, C:Y.844, B:Y.587 CLR.51: 5 residues within 4Å: Chain B: Y.566 Chain C: V.817, F.824, A.828 Ligands: POV.49 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.817, C:F.824, C:A.828, B:Y.566 CLR.53: 6 residues within 4Å: Chain C: Y.587, L.631 Chain D: L.609, E.841, Y.844 Ligands: POV.37 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.609, D:E.841, D:Y.844, C:L.631 CLR.54: 5 residues within 4Å: Chain C: Y.566, L.569 Chain D: V.817, F.824, I.825 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.817, D:F.824, D:I.825, C:Y.566

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

NAG.43: 5 residues within 4Å: Chain B: N.378, T.380, N.381 Ligands: MAN-NAG-BMA-MAN-NAG-NAG.10, MAN-NAG-BMA-MAN-NAG-NAG.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.380, B:T.380 NAG.52: 3 residues within 4Å: Chain C: E.250, G.273, N.275 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.60: 4 residues within 4Å: Chain E: E.8, D.10, D.19, H.24 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.8, E:E.8, E:D.10, E:D.19, E:H.24 ZN.62: 4 residues within 4Å: Chain F: E.8, D.10, D.19, H.24 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.8, F:E.8, F:D.10, F:D.19, F:D.19

2 x CA: CALCIUM ION(Non-covalent)

CA.61: 3 residues within 4Å: Chain E: N.14, D.208, R.228 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.208, E:R.228 CA.63: 4 residues within 4Å: Chain F: D.10, Y.12, N.14, D.208 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.10, F:Y.12, F:D.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gangwar, S.P. et al., Kainate receptor channel opening and gating mechanism. Nature (2024)

Release Date

2024-05-22

Peptides

Glutamate receptor ionotropic, kainate 2: ABCD
Concanavalin A: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

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

Concanavalin A

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