SMTL ID : 8sda.1

CryoEM structure of rat Kv2.1(1-598) L403A mutant in nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

POV.1: 9 residues within 4Å: Chain A: Y.326, N.327, G.330, L.331 Chain B: S.312, T.313, G.314, K.422 Ligands: POV.10 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.312, B:T.313, B:G.314, A:N.327 Salt bridges: B:K.422 POV.2: 10 residues within 4Å: Chain A: P.259, L.260, L.306, A.309, L.315, Q.316, G.319, F.320, R.323 Chain C: A.398 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.398, A:R.323 Hydrogen bonds: A:Q.316 POV.3: 9 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 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.336, A:I.340, A:F.366, A:T.370, C:L.386 POV.4: 4 residues within 4Å: Chain A: L.386 Chain B: L.336, P.363, T.370 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.336, A:L.386 POV.5: 3 residues within 4Å: Chain A: I.194, H.311 Ligands: POV.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.194 POV.6: 12 residues within 4Å: Chain A: H.311, S.312, T.313, G.314, Y.418, K.422 Chain C: N.327, G.330, L.331, I.333, L.334 Ligands: POV.5 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:T.313, A:G.314, A:Y.418, C:N.327, C:L.334 Salt bridges: A:K.422 Hydrophobic interactions: C:L.331 POV.10: 7 residues within 4Å: Chain A: L.334 Chain B: I.194, V.198, L.308, H.311, S.312 Ligands: POV.1 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.194, B:V.198, B:L.308, B:L.308, A:L.334, A:L.334 POV.11: 9 residues within 4Å: Chain B: Y.326, N.327, G.330, L.331 Chain D: S.312, T.313, G.314, Y.418 Ligands: POV.17 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.312, D:T.313, D:G.314, D:Y.418 POV.12: 9 residues within 4Å: Chain B: P.259, L.260, L.306, A.309, L.315, Q.316, L.318, G.319, F.320 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.260, B:L.306, B:A.309, B:L.315, B:Q.316, B:L.318 Hydrogen bonds: B:Q.316, B:F.320 POV.14: 11 residues within 4Å: Chain C: P.259, L.260, L.315, Q.316, G.319, F.320 Chain D: F.335, M.338, G.339, I.342, F.343 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.315, D:F.335, D:F.335, D:I.342, D:F.343 Hydrogen bonds: C:L.260 POV.15: 3 residues within 4Å: Chain C: P.363, T.370 Chain D: L.386 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.386 POV.16: 5 residues within 4Å: Chain C: I.194, V.198, L.308, H.311, S.312 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.198, C:L.308 POV.17: 3 residues within 4Å: Chain D: I.194, V.198 Ligands: POV.11 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.194, D:V.198 POV.18: 9 residues within 4Å: Chain D: P.259, L.260, I.263, L.306, A.309, L.315, Q.316, G.319, F.320 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.263, D:L.306, D:L.315 POV.19: 4 residues within 4Å: Chain B: L.386, K.389 Chain D: P.363, T.370 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:T.370, B:L.386

4 x K: POTASSIUM ION(Non-covalent)

K.7: 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.13 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 interactions with chain D, 1 interactions with chain C Metal complexes: A:V.376, B:T.375, D:T.375, D:V.376, C:T.375 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 D, 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: D:G.377, C:V.376, C:G.377, A:V.376, B:V.376 K.9: 9 residues within 4Å: Chain A: G.377, Y.378 Chain B: G.377, Y.378 Chain C: G.377, Y.378 Chain D: G.377, Y.378 Ligands: K.8 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Metal complexes: C:G.377, C:Y.378, A:Y.378 K.13: 5 residues within 4Å: Chain A: T.375 Chain B: T.375 Chain C: T.375 Chain D: T.375 Ligands: K.7 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Metal complexes: B:T.375, C:T.375, D: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
D

D
C

Membrane

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