SMTL ID : 8qz4.1

Crystal structure of human two pore domain potassium ion channel TREK-2 (K2P10.1) in complex with an activatory nanobody (Nb76)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-2-2-mer

Ligands

4 x BA: BARIUM ION(Non-covalent)(Non-functional Binders)

BA.1: 8 residues within 4Å: Chain A: G.109, Y.110, G.218, F.219 Chain B: G.109, Y.110, G.218, F.219 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:G.109, A:Y.110, A:G.218, B:Y.110, B:G.218 BA.2: 8 residues within 4Å: Chain A: T.107, I.108, T.216, V.217 Chain B: T.107, I.108, T.216, V.217 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:I.108, B:T.216, B:V.217, A:I.108, A:T.216 BA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) BA.7: 2 residues within 4Å: Chain B: K.164, Q.165 No protein-ligand interaction detected (PLIP)

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 11 residues within 4Å: Chain A: L.146, I.149, V.186, F.187, I.194, F.195, L.239, V.240, F.242, W.243, V.246 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.146, A:I.149, A:V.186, A:V.186, A:F.187, A:I.194, A:F.195, A:L.239, A:L.239, A:V.240, A:F.242, A:F.242, A:W.243, A:V.246 Y01.4: 9 residues within 4Å: Chain A: V.18, Y.22, L.262, L.265, S.266 Chain B: F.123, L.126, Y.127, F.130 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.123, B:L.126, B:F.130, A:V.18 Y01.5: 9 residues within 4Å: Chain A: F.123, L.126, Y.127, F.130 Chain B: V.18, Y.22, L.262, L.265, S.266 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.123, A:L.126, A:F.130, B:V.18 Y01.8: 12 residues within 4Å: Chain B: L.146, I.149, S.153, V.186, F.187, I.194, F.195, L.239, V.240, F.242, W.243, V.246 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.146, B:I.149, B:V.186, B:V.186, B:F.187, B:I.194, B:F.195, B:L.239, B:L.239, B:L.239, B:V.240, B:F.242, B:F.242, B:W.243, B:V.246 Hydrogen bonds: B:S.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodstrom, K.E.J. et al., Extracellular modulation of TREK-2 activity with nanobodies provides insight into the mechanisms of K2P channel regulation. Nat Commun (2024)

Release Date

2024-05-29

Peptides

Potassium channel subfamily K member 10: AB
Nanobody 76: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Potassium channel subfamily K member 10

Nanobody 76

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