SMTL ID : 6nf4.1

Structure of zebrafish Otop1 in nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 13 residues within 4Å: Chain A: E.54, A.58, V.202, L.206, I.271, S.274, F.278, W.281 Chain B: T.381, T.384, L.388 Ligands: Y01.3, Y01.7 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.58, A:V.202, A:L.206, A:I.271, A:F.278, A:F.278, B:T.384 Salt bridges: A:K.51 Y01.3: 10 residues within 4Å: Chain A: V.69, L.73, A.76, C.210, M.214 Chain B: V.557 Ligands: Y01.1, Y01.4, Y01.7, Y01.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.69, A:L.73 Y01.4: 10 residues within 4Å: Chain A: L.392, L.396, S.556, T.560, V.564 Chain B: L.66, L.73 Ligands: Y01.3, Y01.5, Y01.8 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.66, B:L.73, A:L.392, A:L.396, A:T.560, A:V.564 Y01.5: 13 residues within 4Å: Chain A: T.381, T.384, L.388 Chain B: E.54, A.58, V.202, L.206, I.271, S.274, F.278, W.281 Ligands: Y01.4, Y01.8 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.58, B:V.202, B:L.206, B:I.271, B:F.278, B:F.278, A:T.384 Salt bridges: B:K.51 Y01.7: 10 residues within 4Å: Chain A: L.66, L.73 Chain B: L.392, L.396, S.556, T.560, V.564 Ligands: Y01.1, Y01.3, Y01.8 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.66, A:L.73, B:L.392, B:L.396, B:T.560, B:V.564 Y01.8: 10 residues within 4Å: Chain A: V.557 Chain B: V.69, L.73, A.76, C.210, M.214 Ligands: Y01.3, Y01.4, Y01.5, Y01.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.69, B:L.73

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 11 residues within 4Å: Chain A: W.127, I.128, G.131, M.134, F.272, W.533, I.534, M.574, H.575, V.577, A.578 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.127, A:W.127, A:W.127, A:I.128, A:F.272, A:W.533, A:W.533, A:I.534, A:M.574, A:V.577, A:A.578 CLR.6: 11 residues within 4Å: Chain B: W.127, I.128, G.131, M.134, F.272, W.533, I.534, M.574, H.575, V.577, A.578 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.127, B:W.127, B:W.127, B:I.128, B:F.272, B:W.533, B:W.533, B:I.534, B:M.574, B:V.577, B:A.578

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saotome, K. et al., Structures of the otopetrin proton channels Otop1 and Otop3. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-06-05

Peptides

Otopetrin1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Otopetrin1