SMTL ID : 6v37.1

K2P2.1(TREK-1)I110D:RuR:ML335 bound channel structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

1 x R2R: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)(Non-covalent)

R2R.1: 4 residues within 4Å: Chain A: D.91, G.127, N.128 Chain B: D.91 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.91, B:D.91, A:D.91, A:D.91, A:D.91, A:D.91, A:G.127

3 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.2: 2 residues within 4Å: Chain A: E.290, H.294 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.290 CD.12: 2 residues within 4Å: Chain B: E.290, H.294 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.290, B:H.294 CD.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x D12: DODECANE(Non-covalent)

D12.3: 3 residues within 4Å: Chain A: L.37, I.41 Ligands: D12.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.37, A:I.41 D12.4: 3 residues within 4Å: Chain A: A.281 Chain B: L.146 Ligands: D12.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.146, A:A.281 D12.5: 5 residues within 4Å: Chain A: I.138, I.142, L.145, L.146 Ligands: HEX.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.142 D12.13: 2 residues within 4Å: Chain B: L.37, I.41 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.37, B:I.41

2 x Q6F: N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl)amino]benzamide(Non-covalent)

Q6F.6: 17 residues within 4Å: Chain A: H.107, G.111, S.112, F.115, G.118, T.119, T.122, F.126, I.129, F.225, A.240, G.241, G.242, K.252, V.255, W.256, I.259 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.115, A:F.115, A:F.115, A:F.126, A:V.255 Hydrogen bonds: A:H.107, A:S.112 pi-Stacking: A:W.256 pi-Cation interactions: A:K.252 Halogen bonds: A:T.122 Q6F.14: 15 residues within 4Å: Chain B: H.107, S.112, F.115, G.118, T.119, F.126, I.129, F.225, A.240, G.241, G.242, K.252, V.255, W.256, I.259 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.115, B:F.115, B:K.252, B:V.255, B:I.259 Hydrogen bonds: B:S.112 pi-Stacking: B:F.115, B:W.256, B:W.256 pi-Cation interactions: B:K.252

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

K.7: 10 residues within 4Å: Chain A: I.124, G.125, I.233, G.234 Chain B: I.124, G.125, I.233, G.234 Ligands: K.8, K.10 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:G.125, B:I.233, A:I.124, A:G.125, A:G.234 K.8: 10 residues within 4Å: Chain A: T.123, I.124, T.232, I.233 Chain B: T.123, I.124, T.232, I.233 Ligands: K.7, K.15 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:T.123, A:T.232, A:I.233, B:T.123, B:I.233 K.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.10: 9 residues within 4Å: Chain A: G.125, F.126, G.234, F.235 Chain B: G.125, F.126, G.234, F.235 Ligands: K.7 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:F.126, A:F.235, B:G.125, B:F.126, B:F.235 K.15: 5 residues within 4Å: Chain A: T.123, T.232 Chain B: T.123, T.232 Ligands: K.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:T.232, A:T.232, B:T.123, B:T.232

1 x HEX: HEXANE(Non-covalent)

HEX.11: 4 residues within 4Å: Chain A: L.145 Chain B: C.200, V.204 Ligands: D12.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pope, L. et al., Polynuclear Ruthenium Amines Inhibit K2PChannels via a "Finger in the Dam" Mechanism. Cell Chem Biol (2020)

Release Date

2020-02-26

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

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