SMTL ID : 7rxg.1

afTMEM16 in C18 lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+, full dimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 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 CA.15: 6 residues within 4Å: Chain B: E.445, D.511, E.514, E.543, D.547, K.550 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.511, B:E.514, B:E.543, B:D.547, H2O.2 CA.16: 3 residues within 4Å: Chain B: E.445, E.514, E.543 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.445, B:E.514, B:E.543, B:E.543, H2O.2

22 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 18 PLIP interactions: 18 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: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.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.384, A:F.388, A:Y.395, A:Y.395 PGW.5: 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.13 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.6: 8 residues within 4Å: Chain A: W.202, R.427, I.431, W.529, L.531, S.535, I.538, N.539 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.7: 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.8: 8 residues within 4Å: Chain A: T.159, F.160, R.189, M.192, A.196, F.197, S.200 Ligands: PGW.9 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.9: 8 residues within 4Å: Chain A: R.189, F.190, F.193, L.218, W.219, V.222, Y.226 Ligands: PGW.8 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.10: 8 residues within 4Å: Chain A: Y.626, A.627, S.630, K.634 Chain B: A.287, Q.364, V.368 Ligands: PGW.14 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.626, A:A.627, B:A.287, B:V.368 Hydrogen bonds: A:Y.626, A:S.630, B:Q.364 Salt bridges: A:K.634, A:K.634 PGW.11: 6 residues within 4Å: Chain A: L.282, P.285, F.286, V.342, L.346, Y.349 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.285, A:V.342 PGW.12: 21 residues within 4Å: Chain A: L.288, F.367, V.368, D.571, G.574, F.575, W.578, V.579, I.582, R.625, R.629 Chain B: F.615, F.616, H.619, L.620, L.622, I.623, R.625, Y.626, R.629 Ligands: PGW.25 21 PLIP interactions: 14 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.288, A:F.367, A:F.367, A:F.575, A:F.575, A:F.575, A:F.575, A:W.578, A:W.578, A:W.578, A:V.579, A:I.582, B:F.615, B:F.616, B:H.619 Hydrogen bonds: A:G.574, A:R.629, B:R.625 Water bridges: B:R.629, B:R.629 Salt bridges: B:R.629 PGW.13: 8 residues within 4Å: Chain A: I.605, R.606, C.607, W.608, L.611 Chain B: W.608, L.612 Ligands: PGW.5 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.611, B:W.608, B:W.608, B:L.612, B:L.612 Hydrogen bonds: A:C.607, A:W.608 PGW.14: 22 residues within 4Å: Chain A: F.615, F.616, H.619, L.620, L.622, I.623, R.625, Y.626, R.629 Chain B: L.288, F.367, V.368, F.371, D.571, G.574, F.575, W.578, V.579, I.582, R.625, R.629 Ligands: PGW.10 22 PLIP interactions: 7 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:F.615, A:F.616, A:H.619, B:L.288, B:F.367, B:F.367, B:F.371, B:F.575, B:F.575, B:F.575, B:F.575, B:W.578, B:W.578, B:W.578, B:V.579, B:I.582 Hydrogen bonds: A:R.625, B:G.574, B:R.629 Water bridges: A:R.629, A:R.629 Salt bridges: A:R.629 PGW.17: 20 residues within 4Å: Chain B: 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 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.210, B:T.213, B:L.218, B:V.588, B:A.609, B:L.612, B:F.616, B:F.616, B:L.620, B:Y.621 Hydrogen bonds: B:Y.589, B:Y.589, B:Y.589, B:S.592, B:S.592, B:N.593, B:N.593 Salt bridges: B:R.606 PGW.18: 6 residues within 4Å: Chain B: V.384, F.388, R.391, I.392, Y.395 Ligands: PGW.20 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.384, B:F.388, B:Y.395, B:Y.395 PGW.19: 8 residues within 4Å: Chain A: W.608, L.612 Chain B: I.605, R.606, C.607, W.608, L.611 Ligands: PGW.20 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.611, A:W.608, A:W.608, A:L.612, A:L.612 Hydrogen bonds: B:C.607, B:W.608 PGW.20: 16 residues within 4Å: Chain B: 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.18, PGW.19 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.371, B:I.379, B:I.379, B:F.383, B:F.383, B:F.383, B:F.383, B:V.384, B:F.388, B:F.388, B:V.579, B:A.586, B:I.605, B:L.610, B:I.614 Hydrogen bonds: B:R.391 PGW.21: 8 residues within 4Å: Chain B: W.202, R.427, I.431, W.529, L.531, S.535, I.538, N.539 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.531, B:I.538, B:N.539 Salt bridges: B:R.427 PGW.22: 8 residues within 4Å: Chain B: L.205, S.207, F.208, S.209, I.210, I.211, V.214, S.592 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.210, B:V.214 Hydrogen bonds: B:I.210, B:I.211, B:S.592 PGW.23: 8 residues within 4Å: Chain B: T.159, F.160, R.189, M.192, A.196, F.197, S.200 Ligands: PGW.24 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.159, B:F.160, B:R.189, B:M.192, B:F.197 PGW.24: 8 residues within 4Å: Chain B: R.189, F.190, F.193, L.218, W.219, V.222, Y.226 Ligands: PGW.23 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.190, B:F.190, B:F.193, B:F.193, B:F.193, B:L.218, B:V.222, B:Y.226, B:Y.226 Salt bridges: B:R.189 PGW.25: 8 residues within 4Å: Chain A: A.287, Q.364, V.368 Chain B: Y.626, A.627, S.630, K.634 Ligands: PGW.12 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.287, A:V.368, B:Y.626, B:A.627 Hydrogen bonds: A:Q.364, B:Y.626, B:S.630 Salt bridges: B:K.634, B:K.634 PGW.26: 6 residues within 4Å: Chain B: L.282, P.285, F.286, V.342, L.346, Y.349 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.285, B:V.342

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Membrane

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

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