SMTL ID : 7rxh.1

afTMEM16 in C18 lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+, monomer with extra lipids

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.445, D.511, E.514, E.543, D.547, K.550 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.511, A:E.514, A:E.543, A:D.547, H2O.1 CA.2: 3 residues within 4Å: Chain A: E.445, E.514, E.543 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.445, A:E.514, A:E.543, A:E.543, H2O.1

16 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

PGW.3: 20 residues within 4Å: Chain A: I.210, T.213, V.214, C.217, L.218, S.585, V.588, Y.589, M.590, S.592, N.593, T.604, R.606, A.609, L.612, T.613, F.616, S.617, L.620, Y.621 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.210, A:T.213, A:L.218, A:V.588, A:A.609, A:L.612, A:F.616, A:F.616, A:L.620, A:Y.621 Hydrogen bonds: A:Y.589, A:Y.589, A:S.592, A:S.592, A:N.593, A:N.593 Salt bridges: A:R.606 PGW.4: 6 residues within 4Å: Chain A: V.384, F.388, R.391, I.392, Y.395 Ligands: PGW.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.384, A:F.388, A:Y.395, A:Y.395 PGW.5: 6 residues within 4Å: Chain A: I.605, R.606, C.607, W.608, L.611 Ligands: PGW.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.611 Hydrogen bonds: A:I.605, A:C.607, A:W.608 PGW.6: 16 residues within 4Å: Chain A: F.371, I.379, F.383, V.384, F.388, R.391, V.579, T.583, A.586, M.590, P.602, I.605, L.610, I.614 Ligands: PGW.4, PGW.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.371, A:I.379, A:I.379, A:F.383, A:F.383, A:F.383, A:F.383, A:V.384, A:F.388, A:F.388, A:V.579, A:A.586, A:I.605, A:L.610, A:I.614 Hydrogen bonds: A:R.391 PGW.7: 9 residues within 4Å: Chain A: W.202, R.427, I.431, W.529, L.531, S.535, I.538, N.539 Ligands: PGW.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.531, A:I.538, A:N.539 Salt bridges: A:R.427 PGW.8: 8 residues within 4Å: Chain A: L.205, S.207, F.208, S.209, I.210, I.211, V.214, S.592 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.210, A:V.214 Hydrogen bonds: A:I.210, A:I.211, A:S.592 PGW.9: 8 residues within 4Å: Chain A: T.159, F.160, R.189, M.192, A.196, F.197, S.200 Ligands: PGW.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.159, A:F.160, A:R.189, A:M.192, A:F.197 PGW.10: 8 residues within 4Å: Chain A: R.189, F.190, F.193, L.218, W.219, V.222, Y.226 Ligands: PGW.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.190, A:F.190, A:F.193, A:F.193, A:F.193, A:L.218, A:V.222, A:Y.226, A:Y.226 Salt bridges: A:R.189 PGW.11: 5 residues within 4Å: Chain A: Y.626, A.627, S.630, K.634 Ligands: PGW.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.626, A:A.627 Hydrogen bonds: A:Y.626, A:S.630 Salt bridges: A:K.634, A:K.634 PGW.12: 8 residues within 4Å: Chain A: L.282, P.285, F.286, V.342, L.346, Y.349 Ligands: PGW.14, PGW.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.285, A:V.342 PGW.13: 10 residues within 4Å: Chain A: F.615, F.616, H.619, L.620, L.622, I.623, R.625, Y.626, R.629 Ligands: PGW.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.615, A:F.616, A:H.619 Hydrogen bonds: A:R.625 Water bridges: A:R.629, A:R.629 Salt bridges: A:R.629 PGW.14: 6 residues within 4Å: Chain A: L.289, V.338, T.341, V.342, K.345 Ligands: PGW.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.289, A:V.342 Salt bridges: A:K.345 PGW.15: 3 residues within 4Å: Chain A: I.439 Ligands: PGW.7, PGW.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.439 PGW.16: 5 residues within 4Å: Chain A: T.325, Y.432, T.436, L.444 Ligands: PGW.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.444 Hydrogen bonds: A:Y.432 PGW.17: 2 residues within 4Å: Chain A: A.330, T.334 No protein-ligand interaction detected (PLIP) PGW.18: 7 residues within 4Å: Chain A: Y.278, R.279, L.281, L.282, P.285, Y.349 Ligands: PGW.12 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.281, A:L.281, A:L.282, A:P.285 Hydrogen bonds: A:R.279, A:Y.349 Salt bridges: A:K.275, A:K.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Falzone, M.E. et al., TMEM16 scramblases thin the membrane to enable lipid scrambling. Nat Commun (2022)

Release Date

2022-05-18

Peptides

afTMEM16 lipid scramblase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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afTMEM16 lipid scramblase

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