SMTL ID : 7rx2.1

afTMEM16 in C22 lipid nanodiscs with MSP1E3 scaffold protein in the presnece of Ca2+

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: Y.180, E.445, D.511, E.514, E.543, D.547 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.445, A:D.511, A:E.543, A:D.547, A:D.547 CA.2: 3 residues within 4Å: Chain A: E.445, E.514, E.543 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.445, A:E.514, A:E.543, A:E.543 CA.11: 6 residues within 4Å: Chain B: Y.180, E.445, D.511, E.514, E.543, D.547 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.445, B:D.511, B:E.543, B:D.547, B:D.547 CA.12: 3 residues within 4Å: Chain B: E.445, E.514, E.543 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.445, B:E.514, B:E.543, B:E.543

14 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: 8 residues within 4Å: Chain A: F.383, F.388, M.590, P.602, I.605, C.607 Chain B: W.608, L.612 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.388, B:W.608, B:W.608, B:L.612 Hydrogen bonds: A:C.607, A:W.608 PGW.4: 18 residues within 4Å: Chain A: I.210, T.213, V.214, C.217, 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, Y.621 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.210, A:T.213, A:V.214, A:V.588, A:Y.589, A:L.612, A:F.616 Hydrogen bonds: A:Y.589, A:Y.589, A:S.592, A:S.592, A:N.593 Salt bridges: A:R.606 PGW.5: 6 residues within 4Å: Chain A: R.189, F.190, F.193, L.218, W.219, Y.226 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.190, A:F.190, A:F.190, A:F.193, A:F.193, A:L.218 Salt bridges: A:R.189 PGW.6: 15 residues within 4Å: Chain A: L.288, F.367, V.368, F.371, D.571, F.575, W.578, V.579, I.582, R.625 Chain B: H.619, L.622, Y.626, R.629 Ligands: PGW.10 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.288, A:F.367, A:V.368, A:F.371, A:D.571, A:F.575, A:F.575, A:F.575, A:W.578, A:V.579, A:I.582 Hydrogen bonds: A:R.625 Salt bridges: B:R.629 PGW.7: 6 residues within 4Å: Chain A: K.275, Y.278, R.279, L.281, L.282, Y.349 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.278, A:Y.278, A:L.281, A:L.281, A:L.282, A:L.282 Hydrogen bonds: A:Y.349 Salt bridges: A:K.275, A:R.279 PGW.8: 7 residues within 4Å: Chain A: P.285, F.286, L.289, V.342, K.345, L.346, Y.349 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.285, A:L.289, A:V.342, A:L.346, A:L.346, A:Y.349, A:Y.349 PGW.9: 8 residues within 4Å: Chain A: Y.626, A.627, S.630, K.634 Chain B: Q.283, A.287, Q.364 Ligands: PGW.16 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.287, B:Q.364 Hydrogen bonds: B:Q.364, B:Q.364, A:S.630 Salt bridges: A:K.634 PGW.10: 8 residues within 4Å: Chain A: Q.283, A.287, Q.364 Chain B: Y.626, A.627, S.630, K.634 Ligands: PGW.6 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.287, A:Q.364 Hydrogen bonds: A:Q.364, A:Q.364 Salt bridges: B:K.634 PGW.13: 8 residues within 4Å: Chain A: W.608, L.612 Chain B: F.383, F.388, M.590, P.602, I.605, C.607 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.388, A:W.608, A:W.608, A:L.612 Hydrogen bonds: B:C.607, B:W.608 PGW.14: 18 residues within 4Å: Chain B: I.210, T.213, V.214, C.217, 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, Y.621 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.210, B:T.213, B:V.214, B:V.588, B:Y.589, B:L.612, B:F.616 Hydrogen bonds: B:Y.589, B:Y.589, B:S.592, B:S.592, B:N.593 Salt bridges: B:R.606 PGW.15: 6 residues within 4Å: Chain B: R.189, F.190, F.193, L.218, W.219, Y.226 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.190, B:F.190, B:F.190, B:F.193, B:F.193, B:L.218 Salt bridges: B:R.189 PGW.16: 17 residues within 4Å: Chain A: F.615, H.619, L.622, I.623, Y.626, R.629 Chain B: L.288, F.367, V.368, F.371, D.571, F.575, W.578, V.579, I.582, R.625 Ligands: PGW.9 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.288, B:F.367, B:V.368, B:F.371, B:D.571, B:F.575, B:F.575, B:F.575, B:W.578, B:V.579, B:I.582, A:F.615, A:I.623 Hydrogen bonds: B:R.625, A:R.625, A:R.629 PGW.17: 6 residues within 4Å: Chain B: K.275, Y.278, R.279, L.281, L.282, Y.349 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.278, B:Y.278, B:L.281, B:L.281, B:L.282, B:L.282 Hydrogen bonds: B:Y.349 Salt bridges: B:K.275, B:R.279 PGW.18: 7 residues within 4Å: Chain B: P.285, F.286, L.289, V.342, K.345, L.346, Y.349 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.285, B:L.289, B:V.342, B:L.346, B:L.346, B:Y.349, B:Y.349

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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