SMTL ID : 8f1c.1

Voltage-gated potassium channel Kv3.1 with novel positive modulator (9M)-9-{5-chloro-6-[(3,3-dimethyl-2,3-dihydro-1-benzofuran-4-yl)oxy]-4-methylpyridin-3-yl}-2-methyl-7,9-dihydro-8H-purin-8-one (compound 4)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.111, C.138, C.139 Chain D: C.117, P.119 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Metal complexes: D:C.117, A:H.111, A:C.138 ZN.8: 5 residues within 4Å: Chain A: C.117, P.119 Chain B: H.111, C.138, C.139 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.111, B:C.138, A:C.117 ZN.11: 5 residues within 4Å: Chain B: C.117, P.119 Chain C: H.111, C.138, C.139 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Metal complexes: B:C.117, C:H.111, C:C.138 ZN.14: 5 residues within 4Å: Chain C: C.117, P.119 Chain D: H.111, C.138, C.139 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Metal complexes: D:H.111, D:C.138, C:C.117

4 x X9T: (9M)-9-{5-chloro-6-[(3,3-dimethyl-2,3-dihydro-1-benzofuran-4-yl)oxy]-4-methylpyridin-3-yl}-2-methyl-7,9-dihydro-8H-purin-8-one(Non-covalent)

X9T.2: 17 residues within 4Å: Chain A: T.395, M.396, Y.398, Y.399, A.400, R.402, I.403, G.404, A.405, Q.406, P.407, S.446, V.450 Chain D: F.343, V.346, F.349 Ligands: POV.3 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:Y.398, A:Y.399, A:A.400, D:F.343, D:V.346 Hydrogen bonds: A:G.404, A:A.405, A:A.405 X9T.9: 17 residues within 4Å: Chain A: F.343, V.346, F.349 Chain B: T.395, M.396, Y.398, Y.399, A.400, R.402, I.403, G.404, A.405, Q.406, P.407, S.446, V.450 Ligands: POV.10 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.398, B:Y.399, B:A.400, A:V.346 Hydrogen bonds: B:G.404, B:A.405, B:A.405 X9T.12: 17 residues within 4Å: Chain B: F.343, V.346, F.349 Chain C: T.395, M.396, Y.398, Y.399, A.400, R.402, I.403, G.404, A.405, Q.406, P.407, S.446, V.450 Ligands: POV.13 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:F.343, B:V.346, C:Y.398, C:Y.399, C:A.400 Hydrogen bonds: C:G.404, C:A.405, C:A.405 X9T.15: 17 residues within 4Å: Chain C: F.343, V.346, F.349 Chain D: T.395, M.396, Y.398, Y.399, A.400, R.402, I.403, G.404, A.405, Q.406, P.407, S.446, V.450 Ligands: POV.16 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.398, D:Y.399, D:A.400, C:F.343, C:V.346 Hydrogen bonds: D:G.404, D:A.405, D:A.405

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

POV.3: 9 residues within 4Å: Chain A: M.396, I.403, G.404, Q.406 Chain D: D.339, F.343, F.349, L.353 Ligands: X9T.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.406 POV.10: 9 residues within 4Å: Chain A: D.339, F.343, F.349, L.353 Chain B: M.396, I.403, G.404, Q.406 Ligands: X9T.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.406 POV.13: 9 residues within 4Å: Chain B: D.339, F.343, F.349, L.353 Chain C: M.396, I.403, G.404, Q.406 Ligands: X9T.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.406 POV.16: 9 residues within 4Å: Chain C: D.339, F.343, F.349, L.353 Chain D: M.396, I.403, G.404, Q.406 Ligands: X9T.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.406

4 x K: POTASSIUM ION(Non-covalent)

K.4: 13 residues within 4Å: Chain A: G.436, Y.437, G.438 Chain B: G.436, Y.437, G.438 Chain C: G.436, Y.437, G.438 Chain D: G.436, Y.437, G.438 Ligands: K.5 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Metal complexes: B:Y.437, C:G.436, C:Y.437, A:Y.437, D:Y.437 K.5: 10 residues within 4Å: Chain A: L.435, G.436 Chain B: L.435, G.436 Chain C: L.435, G.436 Chain D: L.435, G.436 Ligands: K.4, K.6 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Metal complexes: B:L.435, B:G.436, C:L.435, C:G.436, A:L.435 K.6: 10 residues within 4Å: Chain A: T.434, L.435 Chain B: T.434, L.435 Chain C: T.434, L.435 Chain D: T.434, L.435 Ligands: K.5, K.7 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D Metal complexes: C:T.434, C:L.435, B:T.434, B:L.435, D:L.435 K.7: 5 residues within 4Å: Chain A: T.434 Chain B: T.434 Chain C: T.434 Chain D: T.434 Ligands: K.6 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D Metal complexes: C:T.434, B:T.434, B:T.434, A:T.434, D:T.434

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y.T. et al., Identification and structural and biophysical characterization of a positive modulator of human Kv3.1 channels. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-10-25

Peptides

Potassium voltage-gated channel subfamily C 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 C member 1

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