SMTL ID : 9cap.1

Structure of the LPD-3 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

18 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)(Non-functional Binders)

PEE.1: 13 residues within 4Å: Chain A: L.816, F.819, M.845, I.852, E.919, R.924, I.926, I.928, V.933 Ligands: PEE.2, PEE.5, PEE.20, PEE.21 Ligand excluded by PLIP PEE.2: 12 residues within 4Å: Chain A: I.928, V.953, I.955, E.965, V.967, I.969, I.974, L.1007 Ligands: PEE.1, PEE.5, R16.16, R16.17 Ligand excluded by PLIP PEE.3: 20 residues within 4Å: Chain A: A.469, W.473, K.476, V.514, M.516, L.543, F.545, Y.563, M.565, G.567, V.624, M.626, F.628, H.630, L.669, F.698, D.702, M.739 Ligands: PEE.19, PEE.25 Ligand excluded by PLIP PEE.4: 18 residues within 4Å: Chain A: W.185, W.189, I.197, F.219, T.226, F.240, F.285, Y.287, Q.289, D.290, L.291, L.292, W.314, K.358, H.361 Ligands: PEE.10, PEE.11, PEE.23 Ligand excluded by PLIP PEE.5: 5 residues within 4Å: Ligands: PEE.1, PEE.2, R16.7, R16.17, PEE.21 Ligand excluded by PLIP PEE.10: 10 residues within 4Å: Chain A: Y.287, Q.289, L.292, W.310, I.360, H.361, W.405 Ligands: PEE.4, PEE.11, PEE.12 Ligand excluded by PLIP PEE.11: 19 residues within 4Å: Chain A: I.204, T.217, V.247, V.249, L.278, L.283, Y.287, W.310, W.314, F.316, H.364, V.366, I.368, I.403, W.405 Ligands: PEE.4, PEE.10, PEE.12, PEE.13 Ligand excluded by PLIP PEE.12: 15 residues within 4Å: Chain A: K.144, V.249, L.277, L.278, L.322, S.323, Y.324, Y.340, I.403, L.404, W.405 Ligands: PEE.10, PEE.11, PEE.13, R16.24 Ligand excluded by PLIP PEE.13: 14 residues within 4Å: Chain A: L.278, F.316, L.322, R.332, Y.336, I.368, M.401, I.403, F.412, W.414, Y.448 Ligands: PEE.11, PEE.12, R16.14 Ligand excluded by PLIP PEE.18: 2 residues within 4Å: Chain A: W.109 Ligands: R16.30 Ligand excluded by PLIP PEE.19: 21 residues within 4Å: Chain A: M.516, L.518, V.536, I.538, V.571, M.573, W.619, T.621, I.673, L.689, L.690, L.693, F.698, T.738, M.739, V.741, V.743, V.745, K.784 Ligands: PEE.3, PEE.20 Ligand excluded by PLIP PEE.20: 21 residues within 4Å: Chain A: W.619, F.682, L.690, K.694, V.750, A.752, M.754, V.780, I.791, V.795, A.798, C.799, A.800, I.814, L.816, F.819, F.821 Ligands: PEE.1, R16.6, PEE.19, PEE.21 Ligand excluded by PLIP PEE.21: 15 residues within 4Å: Chain A: F.682, V.687, F.691, M.754, V.773, A.800, I.814, I.868, M.869, L.872, V.876 Ligands: PEE.1, PEE.5, R16.6, PEE.20 Ligand excluded by PLIP PEE.22: 12 residues within 4Å: Chain A: I.378, T.391, W.458, I.460, Y.462, F.479, W.486, I.487, F.500, V.502, F.551 Ligands: R16.24 Ligand excluded by PLIP PEE.23: 8 residues within 4Å: Chain A: P.181, V.184, W.185, M.188, W.189, L.192, V.195 Ligands: PEE.4 Ligand excluded by PLIP PEE.25: 13 residues within 4Å: Chain A: Y.462, K.476, T.480, I.483, N.504, M.506, F.545, L.549, F.551, Y.563, Y.632, Y.735 Ligands: PEE.3 Ligand excluded by PLIP PEE.27: 4 residues within 4Å: Chain A: F.38, F.42, L.49 Chain B: Q.30 Ligand excluded by PLIP PEE.29: 8 residues within 4Å: Chain A: V.39, V.40, S.44, S.74, I.75, S.76, K.82 Chain B: W.24 Ligand excluded by PLIP

12 x R16: HEXADECANE(Non-covalent)(Non-functional Binders)

R16.6: 7 residues within 4Å: Chain A: F.682, V.687, L.690, F.691, K.694 Ligands: PEE.20, PEE.21 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.682, A:V.687, A:V.687, A:L.690, A:F.691, A:F.691, A:F.691, A:K.694 R16.7: 4 residues within 4Å: Chain A: L.873, I.877 Ligands: PEE.5, R16.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.877 R16.8: 7 residues within 4Å: Chain A: A.862, M.869, E.870, L.873, F.937, R.1279 Ligands: R16.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.862, A:M.869, A:E.870, A:L.873, A:F.937 R16.9: 3 residues within 4Å: Chain A: A.862, H.866, I.1268 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.862, A:H.866, A:I.1268 R16.14: 10 residues within 4Å: Chain A: N.140, N.141, V.206, L.215, L.277, R.332, I.335, F.339, Y.340 Ligands: PEE.13 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.206, A:L.215, A:L.215, A:L.277, A:R.332, A:R.332, A:I.335, A:F.339 R16.15: 7 residues within 4Å: Chain A: I.70, F.85, V.88, Y.90, I.97, V.99 Ligands: R16.26 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.70, A:F.85, A:V.88, A:Y.90, A:I.97, A:V.99 R16.16: 2 residues within 4Å: Chain A: I.974 Ligands: PEE.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.974 R16.17: 2 residues within 4Å: Ligands: PEE.2, PEE.5 No protein-ligand interaction detected (PLIP) R16.24: 7 residues within 4Å: Chain A: Y.324, E.329, Q.456, V.498, F.500 Ligands: PEE.12, PEE.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.498, A:F.500 R16.26: 3 residues within 4Å: Chain A: F.68, Y.90 Ligands: R16.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.68, A:F.68, A:Y.90 R16.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) R16.30: 2 residues within 4Å: Chain A: H.79 Ligands: PEE.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, S.A. et al., Structural basis of bulk lipid transfer by bridge-like lipid transfer protein LPD-3. To Be Published

Release Date

2025-04-23

Peptides

Bridge-like lipid transfer protein family member 1 C-terminal domain-containing protein: A
Defect at low temperature protein 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Bridge-like lipid transfer protein family member 1 C-terminal domain-containing protein

Defect at low temperature protein 1