SMTL ID : 8sd3.1

CryoEM structure of rat Kv2.1(1-598) wild type in nanodiscs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

POV.1: 14 residues within 4Å: Chain A: Y.326, N.327, L.329, G.330, L.331, I.333, L.334, A.337 Chain B: H.311, S.312, T.313, G.314, Y.418 Ligands: POV.10 Ligand excluded by PLIP POV.2: 15 residues within 4Å: Chain A: P.259, L.260, I.263, L.306, A.309, L.315, Q.316, L.318, G.319, F.320, L.322, R.323, Q.421 Chain C: F.335, M.338 Ligand excluded by PLIP POV.3: 11 residues within 4Å: Chain A: A.337, I.340, M.341, P.363, F.366 Chain B: T.201, I.202, S.205, L.206 Chain C: L.386, I.390 Ligand excluded by PLIP POV.4: 12 residues within 4Å: Chain A: L.336, I.340, P.363, A.364, F.366, W.367, T.370 Chain C: L.386, K.389, I.390, G.393, L.394 Ligand excluded by PLIP POV.5: 3 residues within 4Å: Chain A: L.322, R.323, Y.326 Ligand excluded by PLIP POV.6: 6 residues within 4Å: Chain A: I.194, L.308, H.311, S.312 Chain C: L.334 Ligands: POV.16 Ligand excluded by PLIP POV.10: 6 residues within 4Å: Chain A: L.334 Chain B: I.194, L.308, H.311, S.312 Ligands: POV.1 Ligand excluded by PLIP POV.11: 14 residues within 4Å: Chain B: Y.326, N.327, L.329, G.330, L.331, I.333, L.334, A.337 Chain D: H.311, S.312, T.313, G.314, Y.418 Ligands: POV.23 Ligand excluded by PLIP POV.12: 15 residues within 4Å: Chain A: F.335, M.338 Chain B: P.259, L.260, I.263, L.306, A.309, L.315, Q.316, L.318, G.319, F.320, L.322, R.323, Q.421 Ligand excluded by PLIP POV.13: 11 residues within 4Å: Chain A: L.386, I.390 Chain B: A.337, I.340, M.341, P.363, F.366 Chain D: T.201, I.202, S.205, L.206 Ligand excluded by PLIP POV.14: 12 residues within 4Å: Chain A: L.386, K.389, I.390, G.393, L.394 Chain B: L.336, I.340, P.363, A.364, F.366, W.367, T.370 Ligand excluded by PLIP POV.15: 3 residues within 4Å: Chain B: L.322, R.323, Y.326 Ligand excluded by PLIP POV.16: 14 residues within 4Å: Chain A: H.311, S.312, T.313, G.314, Y.418 Chain C: Y.326, N.327, L.329, G.330, L.331, I.333, L.334, A.337 Ligands: POV.6 Ligand excluded by PLIP POV.17: 15 residues within 4Å: Chain C: P.259, L.260, I.263, L.306, A.309, L.315, Q.316, L.318, G.319, F.320, L.322, R.323, Q.421 Chain D: F.335, M.338 Ligand excluded by PLIP POV.18: 11 residues within 4Å: Chain A: T.201, I.202, S.205, L.206 Chain C: A.337, I.340, M.341, P.363, F.366 Chain D: L.386, I.390 Ligand excluded by PLIP POV.19: 12 residues within 4Å: Chain C: L.336, I.340, P.363, A.364, F.366, W.367, T.370 Chain D: L.386, K.389, I.390, G.393, L.394 Ligand excluded by PLIP POV.20: 3 residues within 4Å: Chain C: L.322, R.323, Y.326 Ligand excluded by PLIP POV.21: 6 residues within 4Å: Chain C: I.194, L.308, H.311, S.312 Chain D: L.334 Ligands: POV.24 Ligand excluded by PLIP POV.23: 6 residues within 4Å: Chain B: L.334 Chain D: I.194, L.308, H.311, S.312 Ligands: POV.11 Ligand excluded by PLIP POV.24: 14 residues within 4Å: Chain C: H.311, S.312, T.313, G.314, Y.418 Chain D: Y.326, N.327, L.329, G.330, L.331, I.333, L.334, A.337 Ligands: POV.21 Ligand excluded by PLIP POV.25: 15 residues within 4Å: Chain B: F.335, M.338 Chain D: P.259, L.260, I.263, L.306, A.309, L.315, Q.316, L.318, G.319, F.320, L.322, R.323, Q.421 Ligand excluded by PLIP POV.26: 11 residues within 4Å: Chain B: L.386, I.390 Chain C: T.201, I.202, S.205, L.206 Chain D: A.337, I.340, M.341, P.363, F.366 Ligand excluded by PLIP POV.27: 12 residues within 4Å: Chain B: L.386, K.389, I.390, G.393, L.394 Chain D: L.336, I.340, P.363, A.364, F.366, W.367, T.370 Ligand excluded by PLIP POV.28: 3 residues within 4Å: Chain D: L.322, R.323, Y.326 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-covalent)

K.7: 13 residues within 4Å: Chain A: G.377, Y.378, G.379 Chain B: G.377, Y.378, G.379 Chain C: G.377, Y.378, G.379 Chain D: G.377, Y.378, G.379 Ligands: K.8 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:G.377, C:Y.378, D:Y.378, B:Y.378, A:Y.378 K.8: 10 residues within 4Å: Chain A: V.376, G.377 Chain B: V.376, G.377 Chain C: V.376, G.377 Chain D: V.376, G.377 Ligands: K.7, K.9 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Metal complexes: C:G.377, A:V.376, A:G.377, B:V.376, D:G.377 K.9: 10 residues within 4Å: Chain A: T.375, V.376 Chain B: T.375, V.376 Chain C: T.375, V.376 Chain D: T.375, V.376 Ligands: K.8, K.22 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Metal complexes: A:T.375, A:V.376, B:V.376, C:T.375, D:T.375 K.22: 5 residues within 4Å: Chain A: T.375 Chain B: T.375 Chain C: T.375 Chain D: T.375 Ligands: K.9 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A Metal complexes: C:T.375, B:T.375, D:T.375, A:T.375

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez-Marino, A.I. et al., Inactivation of the Kv2.1 channel through electromechanical coupling. Nature (2023)

Release Date

2023-09-27

Peptides

Potassium voltage-gated channel subfamily B member 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Potassium voltage-gated channel subfamily B member 1