SMTL ID : 8qud.1

Cryo-EM Structure of Human Kv3.1 in Complex with Modulator AUT5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x WY0: (5R)-5-ethyl-3-(6-spiro[2H-1-benzofuran-3,1'-cyclopropane]-4-yloxypyridin-3-yl)imidazolidine-2,4-dione(Non-covalent)

WY0.1: 11 residues within 4Å: Chain A: M.362, Y.365, A.366, R.368, I.369, G.370, A.371, Q.372, P.373 Chain B: V.312, F.315 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.365, A:Y.365, A:A.366, A:I.369, B:V.312, B:V.312, B:F.315, B:F.315 Hydrogen bonds: A:G.370, A:A.371, A:A.371 WY0.8: 11 residues within 4Å: Chain B: M.362, Y.365, A.366, R.368, I.369, G.370, A.371, Q.372, P.373 Chain D: V.312, F.315 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:Y.365, B:Y.365, B:A.366, B:I.369, D:V.312, D:V.312, D:F.315, D:F.315 Hydrogen bonds: B:G.370, B:A.371, B:A.371 WY0.14: 11 residues within 4Å: Chain A: V.312, F.315 Chain C: M.362, Y.365, A.366, R.368, I.369, G.370, A.371, Q.372, P.373 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:Y.365, C:Y.365, C:A.366, C:I.369, A:V.312, A:V.312, A:F.315, A:F.315 Hydrogen bonds: C:G.370, C:A.371, C:A.371 WY0.18: 11 residues within 4Å: Chain C: V.312, F.315 Chain D: M.362, Y.365, A.366, R.368, I.369, G.370, A.371, Q.372, P.373 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.365, D:Y.365, D:A.366, D:I.369, C:V.312, C:V.312, C:F.315, C:F.315 Hydrogen bonds: D:G.370, D:A.371, D:A.371

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.77, C.104, C.105 Chain B: C.83 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.77, A:C.104, A:C.105, B:C.83 ZN.9: 4 residues within 4Å: Chain B: H.77, C.104, C.105 Chain D: C.83 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Metal complexes: B:H.77, B:C.104, B:C.105, D:C.83 ZN.15: 4 residues within 4Å: Chain A: C.83 Chain C: H.77, C.104, C.105 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.77, C:C.104, C:C.105, A:C.83 ZN.19: 4 residues within 4Å: Chain C: C.83 Chain D: H.77, C.104, C.105 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Metal complexes: D:H.77, D:C.104, D:C.105, C:C.83

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 13 residues within 4Å: Chain A: N.276, L.278, F.322, R.326, L.331, R.332, L.334, G.335, L.338 Chain C: F.351, L.354, G.355, I.358 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.322, A:F.322, A:R.326, A:R.332, A:L.338, C:L.354, C:I.358 Hydrogen bonds: A:N.276, A:N.276 Y01.10: 13 residues within 4Å: Chain A: F.351, L.354, G.355, I.358 Chain B: N.276, L.278, F.322, R.326, L.331, R.332, L.334, G.335, L.338 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.354, A:I.358, B:F.322, B:F.322, B:R.326, B:R.332, B:L.338 Hydrogen bonds: B:N.276, B:N.276 Y01.16: 13 residues within 4Å: Chain C: N.276, L.278, F.322, R.326, L.331, R.332, L.334, G.335, L.338 Chain D: F.351, L.354, G.355, I.358 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:L.354, D:I.358, C:F.322, C:F.322, C:R.326, C:R.332, C:L.338 Hydrogen bonds: C:N.276, C:N.276 Y01.20: 13 residues within 4Å: Chain B: F.351, L.354, G.355, I.358 Chain D: N.276, L.278, F.322, R.326, L.331, R.332, L.334, G.335, L.338 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:F.322, D:F.322, D:R.326, D:R.332, D:L.338, B:L.354, B:I.358 Hydrogen bonds: D:N.276, D:N.276

4 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE(Non-covalent)

PCF.4: 12 residues within 4Å: Chain A: I.204, T.205, L.209, H.212, R.214 Chain C: P.388, I.389, V.395 Chain D: Q.409, T.410, W.411, M.414 9 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:I.204, A:L.209, C:P.388, C:P.388, C:I.389, C:V.395, D:W.411 Salt bridges: A:H.212, A:R.214 PCF.11: 12 residues within 4Å: Chain A: P.388, I.389, V.395 Chain B: I.204, T.205, L.209, H.212, R.214 Chain C: Q.409, T.410, W.411, M.414 9 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:I.204, B:L.209, A:P.388, A:P.388, A:I.389, A:V.395, C:W.411 Salt bridges: B:H.212, B:R.214 PCF.13: 12 residues within 4Å: Chain B: Q.409, T.410, W.411, M.414 Chain C: I.204, T.205, L.209, H.212, R.214 Chain D: P.388, I.389, V.395 10 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:P.388, D:P.388, D:I.389, D:V.395, C:I.204, C:L.209, B:W.411 Salt bridges: C:H.212, C:R.214, C:R.214 PCF.17: 12 residues within 4Å: Chain A: Q.409, T.410, W.411, M.414 Chain B: P.388, I.389, V.395 Chain D: I.204, T.205, L.209, H.212, R.214 9 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: B:P.388, B:P.388, B:I.389, B:V.395, A:W.411, D:I.204, D:L.209 Salt bridges: D:H.212, D:R.214

6 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.5: 10 residues within 4Å: Chain A: T.400, L.401 Chain B: T.400, L.401 Chain C: T.400, L.401 Chain D: T.400, L.401 Ligands: K.21, K.22 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Metal complexes: A:T.400, C:T.400, D:T.400, B:T.400 K.6: 1 residues within 4Å: Ligands: K.22 No protein-ligand interaction detected (PLIP) K.7: 5 residues within 4Å: Chain A: Y.403 Chain B: Y.403 Chain C: Y.403 Chain D: Y.403 Ligands: K.12 No protein-ligand interaction detected (PLIP) K.12: 10 residues within 4Å: Chain A: G.402, Y.403 Chain B: G.402, Y.403 Chain C: G.402, Y.403 Chain D: G.402, Y.403 Ligands: K.7, K.21 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:Y.403, D:Y.403, A:Y.403, B:Y.403 K.21: 10 residues within 4Å: Chain A: L.401, G.402 Chain B: L.401, G.402 Chain C: L.401, G.402 Chain D: L.401, G.402 Ligands: K.5, K.12 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Metal complexes: C:L.401, C:G.402, A:L.401, B:L.401, D:L.401 K.22: 6 residues within 4Å: Chain A: T.400 Chain B: T.400 Chain C: T.400 Chain D: T.400 Ligands: K.5, K.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, Q. et al., The binding and mechanism of a positive allosteric modulator of Kv3 channels. Nat Commun (2024)

Release Date

2024-04-03

Peptides

Potassium voltage-gated channel subfamily C 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 C member 1

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