SMTL ID : 8quc.1

Cryo-EM Structure of Human Kv3.1 in Complex with Modulator AUT1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x WY9: (5R)-5-ethyl-3-[6-(3-methoxy-4-methyl-phenoxy)pyridin-3-yl]imidazolidine-2,4-dione(Non-covalent)

WY9.1: 12 residues within 4Å: Chain A: M.362, Y.365, A.366, R.368, I.369, G.370, A.371, Q.372, P.373, V.416 Chain B: V.312, F.315 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:M.362, A:Y.365, A:A.366, A:I.369, A:V.416, B:V.312, B:V.312 Hydrogen bonds: A:G.370, A:A.371, A:A.371 WY9.12: 12 residues within 4Å: Chain B: M.362, Y.365, A.366, R.368, I.369, G.370, A.371, Q.372, P.373, V.416 Chain D: V.312, F.315 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:M.362, B:Y.365, B:A.366, B:I.369, B:V.416, D:V.312, D:V.312 Hydrogen bonds: B:G.370, B:A.371, B:A.371 WY9.16: 12 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, V.416 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:M.362, C:Y.365, C:A.366, C:I.369, C:V.416, A:V.312 Hydrogen bonds: C:G.370, C:A.371, C:A.371 WY9.19: 12 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, V.416 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:M.362, D:Y.365, D:A.366, D:I.369, D:V.416, C:V.312, C:V.312 Hydrogen bonds: D:G.370, D:A.371, D:A.371

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

PCF.2: 13 residues within 4Å: Chain A: Q.409, T.410, W.411, M.414, L.415 Chain B: L.352, P.388, I.389 Chain D: I.204, T.205, L.209, H.212, R.214 14 PLIP interactions: 6 interactions with chain D, 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: D:I.204, D:T.205, D:L.209, A:W.411, A:M.414, A:L.415, B:L.352, B:P.388, B:P.388, B:I.389 Salt bridges: D:H.212, D:H.212, D:R.214 Hydrogen bonds: A:W.411 PCF.5: 12 residues within 4Å: Chain A: L.352, P.388, I.389 Chain B: I.204, L.209, H.212, R.214 Chain C: Q.409, T.410, W.411, M.414, L.415 13 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: C:W.411, C:M.414, C:L.415, A:L.352, A:P.388, A:P.388, A:I.389, B:I.204, B:L.209 Hydrogen bonds: C:W.411 Salt bridges: B:H.212, B:H.212, B:R.214 PCF.6: 13 residues within 4Å: Chain A: I.204, T.205, L.209, H.212, R.214 Chain C: L.352, P.388, I.389 Chain D: Q.409, T.410, W.411, M.414, L.415 14 PLIP interactions: 6 interactions with chain A, 4 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: A:I.204, A:T.205, A:L.209, D:W.411, D:M.414, D:L.415, C:L.352, C:P.388, C:P.388, C:I.389 Salt bridges: A:H.212, A:H.212, A:R.214 Hydrogen bonds: D:W.411 PCF.13: 14 residues within 4Å: Chain B: Q.409, T.410, W.411, M.414, L.415 Chain C: I.204, L.209, H.212, R.214 Chain D: L.352, P.388, I.389, F.391, W.392 15 PLIP interactions: 6 interactions with chain D, 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: D:L.352, D:P.388, D:P.388, D:I.389, D:F.391, D:W.392, B:W.411, B:M.414, B:L.415, C:I.204, C:L.209 Hydrogen bonds: B:W.411 Salt bridges: C:H.212, C:H.212, C:R.214

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.77, C.104, C.105 Chain B: C.83 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:C.83, A:H.77, A:C.104, A:C.105 ZN.14: 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.17: 4 residues within 4Å: Chain A: C.83 Chain C: H.77, C.104, C.105 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Metal complexes: A:C.83, C:H.77, C:C.104, C:C.105 ZN.20: 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)

Y01.4: 12 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, G.355, T.427 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.278, A:F.322, A:F.322, A:L.338, C:F.351 Hydrogen bonds: A:N.276 Y01.15: 12 residues within 4Å: Chain A: F.351, G.355, T.427 Chain B: N.276, L.278, F.322, R.326, L.331, R.332, L.334, G.335, L.338 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.278, B:F.322, B:F.322, B:L.338, A:F.351 Hydrogen bonds: B:N.276 Y01.18: 12 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, G.355, T.427 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:F.351, C:L.278, C:F.322, C:F.322, C:L.338 Hydrogen bonds: C:N.276 Y01.21: 12 residues within 4Å: Chain B: F.351, G.355, T.427 Chain D: N.276, L.278, F.322, R.326, L.331, R.332, L.334, G.335, L.338 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.278, D:F.322, D:F.322, D:L.338, B:F.351 Hydrogen bonds: D:N.276

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

K.7: 9 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.8 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: D:Y.403, C:Y.403, B:Y.403, A:Y.403 K.8: 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.7, K.9 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Metal complexes: B:L.401, B:G.402, C:L.401, D:L.401, A:L.401 K.9: 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.8, K.10 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:L.401, D:L.401, A:L.401, B:L.401 K.10: 5 residues within 4Å: Chain A: T.400 Chain B: T.400 Chain C: T.400 Chain D: T.400 Ligands: K.9 No protein-ligand interaction detected (PLIP) K.11: 0 residues within 4Å: (No contacts) 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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