SMTL ID : 8uf6.1

Structure of Trek-1(K2P2.1) with ML336

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x WRZ: N-[(2,4-dichlorophenyl)methyl]-4-propanamidobenzamide

WRZ.1: 20 residues within 4Å: Chain A: S.91, H.92, D.94, S.97, F.100, G.103, T.104, T.107, F.111, N.113, I.114, F.210, V.224, A.225, G.226, G.227, K.237, V.240, W.241, I.244 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.100, A:F.111, A:I.114, A:V.224, A:K.237, A:I.244 Hydrogen bonds: A:S.97 pi-Stacking: A:F.100, A:F.100, A:W.241, A:W.241 Halogen bonds: A:T.107 WRZ.8: 16 residues within 4Å: Chain B: S.91, S.97, F.100, G.103, T.104, T.107, F.111, N.113, I.114, A.225, G.226, K.237, V.240, W.241, I.244 Ligands: 1PE.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.100, B:F.111, B:I.114, B:K.237, B:I.244 Hydrogen bonds: B:S.97, B:N.113 pi-Stacking: B:F.100, B:F.100, B:W.241, B:W.241 Halogen bonds: B:T.107

2 x D10: DECANE(Non-covalent)

D10.2: 2 residues within 4Å: Chain A: L.191, V.239 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.191, A:V.239 D10.3: 1 residues within 4Å: Chain A: G.120 No protein-ligand interaction detected (PLIP)

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

K.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.5: 10 residues within 4Å: Chain A: I.109, G.110, I.218, G.219 Chain B: I.109, G.110, I.218, G.219 Ligands: K.11, K.12 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:G.110, B:I.218, A:I.109, A:I.218, A:G.219 K.6: 5 residues within 4Å: Chain A: T.108, T.217 Chain B: T.108, T.217 Ligands: K.12 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:T.217, A:T.217, B:T.108, B:T.217, B:T.217 K.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.11: 9 residues within 4Å: Chain A: G.110, F.111, G.219, F.220 Chain B: G.110, F.111, G.219, F.220 Ligands: K.5 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:F.111, A:F.220, B:F.111, B:F.220 K.12: 10 residues within 4Å: Chain A: T.108, I.109, T.217, I.218 Chain B: T.108, I.109, T.217, I.218 Ligands: K.5, K.6 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:I.109, A:T.217, B:I.109, B:T.217, B:I.218

2 x 16C: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE(Non-covalent)

16C.7: 6 residues within 4Å: Chain A: Y.23, I.26, I.265, A.266, T.269, K.270 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.23, A:Y.23, A:I.26, A:I.26, A:I.265, A:A.266 Hydrogen bonds: A:T.269, A:T.269 16C.16: 7 residues within 4Å: Chain A: I.127, L.131 Chain B: C.185, A.204, L.205, I.208, I.265 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.127, B:I.265

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 9 residues within 4Å: Chain B: V.90, D.94, G.96, S.97, F.99, K.237, P.238, W.241 Ligands: WRZ.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.97

2 x CD: CADMIUM ION(Non-covalent)

CD.13: 1 residues within 4Å: Chain B: Q.89 No protein-ligand interaction detected (PLIP) CD.14: 2 residues within 4Å: Chain B: E.275, H.279 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.275, B:H.279

1 x D12: DODECANE(Non-covalent)

D12.15: 1 residues within 4Å: Chain B: A.266 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.266

2 x OCT: N-OCTANE(Non-functional Binders)(Non-covalent)

OCT.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.18: 5 residues within 4Å: Chain B: P.192, I.195, V.239, V.240, W.243 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.192, B:I.195, B:I.195, B:V.240, B:W.243

1 x R16: HEXADECANE(Non-covalent)

R16.19: 3 residues within 4Å: Chain B: Y.23, I.26, K.270 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.23, B:I.26, B:K.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lolicato, M. et al., Structure of Trek-1(K2P2.1) with ML336. To Be Published

Release Date

2024-06-26

Peptides

Potassium channel subfamily K member 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Potassium channel subfamily K member 2