SMTL ID : 1lsh.1

LIPID-PROTEIN INTERACTIONS IN LIPOVITELLIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

7 x PLD: di-heneicosanoyl phosphatidyl choline(Non-covalent)

PLD.1: 20 residues within 4Å: Chain A: Y.171, T.173, T.176, A.177, A.179, L.192, L.222, A.428, M.651, Y.653, Y.791, L.803, L.805, A.854, I.855, M.867, T.869, Y.871 Ligands: PLD.2, PLD.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.176, A:L.192, A:L.222, A:Y.653, A:Y.791, A:L.803, A:L.805, A:L.805, A:A.854, A:Y.871 Hydrogen bonds: A:Y.171, A:T.173 Water bridges: A:T.176, A:Y.653 PLD.2: 11 residues within 4Å: Chain A: F.225, A.622, G.623, G.648, Q.649, G.650, I.1027 Ligands: PLD.1, PLD.6, UPL.20, UPL.30 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.225 PLD.3: 17 residues within 4Å: Chain A: G.604, C.605, K.609, V.611, V.613, A.626, Y.628, R.630, A.644, K.645, I.646, V.658, F.660 Chain B: F.222, T.223, F.224 Ligands: UPL.25 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.613, A:A.626, A:Y.628, A:Y.628, A:Y.628, A:A.644, A:I.646, A:F.660, A:F.660, B:F.222, B:F.222 Hydrogen bonds: A:G.604 Salt bridges: A:K.609, A:R.630, A:R.630 PLD.4: 18 residues within 4Å: Chain A: G.175, Y.178, A.380, S.381, S.384, N.385, S.421, R.425, V.729, H.730, Q.732, V.734, K.782, Y.784, V.785, E.788, M.848 Ligands: UPL.15 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.178, A:A.380, A:Q.732, A:V.734, A:K.782, A:Y.784 Hydrogen bonds: A:N.385, A:E.788 Water bridges: A:G.175, A:Y.178, A:R.425, A:R.425, A:R.425, A:E.788, A:E.788 Salt bridges: A:R.425, A:R.425 PLD.5: 11 residues within 4Å: Chain A: Q.377, V.778, L.780, N.813, A.815, L.877, V.879 Ligands: UPL.11, UPL.15, UPL.17, UPL.21 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.778, A:A.815, A:L.877, A:V.879 Hydrogen bonds: A:Q.377 PLD.6: 12 residues within 4Å: Chain A: S.655, D.656, I.657, V.658, V.727, V.729, H.730, S.787, L.805 Ligands: PLD.1, PLD.2, UPL.25 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.658, A:V.727, A:V.729, A:L.805 Hydrogen bonds: A:S.655 Salt bridges: A:H.730 PLD.37: 12 residues within 4Å: Chain A: R.576 Chain B: L.176, M.178, M.202, I.204, Y.213, G.217, I.218, L.219 Ligands: UPL.8, UPL.42, UPL.49 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.176, B:I.204, B:Y.213, B:I.218 Hydrogen bonds: B:L.219, A:R.576

43 x UPL: UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID(Non-covalent)(Non-functional Binders)

UPL.7: 3 residues within 4Å: Chain A: Q.850, T.873, S.908 Ligand excluded by PLIP UPL.8: 7 residues within 4Å: Chain A: S.578, D.614, T.615, V.624, A.626 Chain B: P.221 Ligands: PLD.37 Ligand excluded by PLIP UPL.9: 7 residues within 4Å: Chain A: A.644, F.660, L.662, Y.726, V.727, V.735, A.737 Ligand excluded by PLIP UPL.10: 9 residues within 4Å: Chain A: L.877, V.905, V.1007, V.1035, V.1037 Ligands: UPL.16, UPL.21, UPL.22, UPL.26 Ligand excluded by PLIP UPL.11: 7 residues within 4Å: Chain A: L.817, V.879, I.883, L.896 Ligands: PLD.5, UPL.14, UPL.21 Ligand excluded by PLIP UPL.12: 12 residues within 4Å: Chain A: Y.12, A.14, L.30, S.31, G.32, M.34, F.77, T.104, T.106, T.860, D.861, L.862 Ligand excluded by PLIP UPL.13: 8 residues within 4Å: Chain A: S.1000 Chain B: I.57, L.59, T.73 Ligands: UPL.18, UPL.38, UPL.39, UPL.47 Ligand excluded by PLIP UPL.14: 6 residues within 4Å: Chain A: V.768, M.776, L.840, I.883 Ligands: UPL.11, UPL.19 Ligand excluded by PLIP UPL.15: 6 residues within 4Å: Chain A: T.811, N.813 Ligands: PLD.4, PLD.5, UPL.16, UPL.21 Ligand excluded by PLIP UPL.16: 7 residues within 4Å: Chain A: N.813, T.846, M.848, A.875, V.906 Ligands: UPL.10, UPL.15 Ligand excluded by PLIP UPL.17: 1 residues within 4Å: Ligands: PLD.5 Ligand excluded by PLIP UPL.18: 5 residues within 4Å: Chain A: K.999, V.1007 Ligands: UPL.13, UPL.35, UPL.38 Ligand excluded by PLIP UPL.19: 5 residues within 4Å: Chain A: L.772, I.838, L.840, M.885 Ligands: UPL.14 Ligand excluded by PLIP UPL.20: 4 residues within 4Å: Chain A: M.910, L.1013, Y.1031 Ligands: PLD.2 Ligand excluded by PLIP UPL.21: 5 residues within 4Å: Ligands: PLD.5, UPL.10, UPL.11, UPL.15, UPL.34 Ligand excluded by PLIP UPL.22: 1 residues within 4Å: Ligands: UPL.10 Ligand excluded by PLIP UPL.23: 6 residues within 4Å: Chain A: P.639, R.640, A.641, V.642, L.662, A.664 Ligand excluded by PLIP UPL.24: 1 residues within 4Å: Chain A: L.638 Ligand excluded by PLIP UPL.25: 3 residues within 4Å: Ligands: PLD.3, PLD.6, UPL.30 Ligand excluded by PLIP UPL.26: 3 residues within 4Å: Chain A: V.1007 Ligands: UPL.10, UPL.32 Ligand excluded by PLIP UPL.27: 3 residues within 4Å: Chain A: T.1047, V.1049 Chain B: L.59 Ligand excluded by PLIP UPL.28: 4 residues within 4Å: Chain A: L.662, S.724, G.725, A.737 Ligand excluded by PLIP UPL.29: 3 residues within 4Å: Chain A: L.1053 Chain B: V.55, L.75 Ligand excluded by PLIP UPL.30: 4 residues within 4Å: Chain A: I.646, I.657 Ligands: PLD.2, UPL.25 Ligand excluded by PLIP UPL.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UPL.32: 1 residues within 4Å: Ligands: UPL.26 Ligand excluded by PLIP UPL.33: 1 residues within 4Å: Ligands: UPL.34 Ligand excluded by PLIP UPL.34: 2 residues within 4Å: Ligands: UPL.21, UPL.33 Ligand excluded by PLIP UPL.35: 3 residues within 4Å: Chain A: C.997, K.999 Ligands: UPL.18 Ligand excluded by PLIP UPL.36: 1 residues within 4Å: Ligands: UPL.47 Ligand excluded by PLIP UPL.38: 8 residues within 4Å: Chain B: L.71, L.102, W.120 Ligands: UPL.13, UPL.18, UPL.40, UPL.47, UPL.50 Ligand excluded by PLIP UPL.39: 1 residues within 4Å: Ligands: UPL.13 Ligand excluded by PLIP UPL.40: 8 residues within 4Å: Chain B: I.118, W.120, A.129, W.150, L.157, K.161 Ligands: UPL.38, UPL.50 Ligand excluded by PLIP UPL.41: 3 residues within 4Å: Chain B: L.157, A.160, L.164 Ligand excluded by PLIP UPL.42: 3 residues within 4Å: Ligands: PLD.37, UPL.43, UPL.49 Ligand excluded by PLIP UPL.43: 2 residues within 4Å: Ligands: UPL.42, UPL.46 Ligand excluded by PLIP UPL.44: 1 residues within 4Å: Ligands: UPL.45 Ligand excluded by PLIP UPL.45: 3 residues within 4Å: Chain B: L.131, I.148 Ligands: UPL.44 Ligand excluded by PLIP UPL.46: 3 residues within 4Å: Chain B: L.131, A.133 Ligands: UPL.43 Ligand excluded by PLIP UPL.47: 4 residues within 4Å: Ligands: UPL.13, UPL.36, UPL.38, UPL.50 Ligand excluded by PLIP UPL.48: 3 residues within 4Å: Chain B: V.190, L.208 Ligands: UPL.49 Ligand excluded by PLIP UPL.49: 4 residues within 4Å: Chain B: V.192 Ligands: PLD.37, UPL.42, UPL.48 Ligand excluded by PLIP UPL.50: 3 residues within 4Å: Ligands: UPL.38, UPL.40, UPL.47 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, J.R. et al., Lipid-protein interactions in lipovitellin. Biochemistry (2002)

Release Date

2002-07-31

Peptides

LIPOVITELLIN (LV-1N, LV-1C): A
LIPOVITELLIN (LV-2): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LIPOVITELLIN (LV-1N, LV-1C)

LIPOVITELLIN (LV-2)