SMTL ID : 8y6i.1

P-glycoprotein in complex with UIC2 Fab and triple elacridar molecules in nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

12 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 8 residues within 4Å: Chain A: T.112, A.115, Y.116, S.119, L.126, F.951, R.958 Ligands: CLR.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.115, A:Y.116, A:L.126, A:F.951, A:F.951 CLR.2: 7 residues within 4Å: Chain A: L.860, I.864, G.955, R.958, F.959, Y.962 Ligands: CLR.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.860, A:I.864, A:R.958, A:F.959, A:F.959, A:Y.962, A:Y.962 CLR.3: 7 residues within 4Å: Chain A: I.836, N.839, I.840, G.844, I.847, S.992 Ligands: CLR.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.836, A:I.840, A:I.847 CLR.4: 6 residues within 4Å: Chain A: L.843, V.865, A.869, V.873, S.992 Ligands: CLR.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.843, A:A.869, A:V.873 CLR.5: 8 residues within 4Å: Chain A: I.221, A.308, L.312, W.315, N.753, L.757, L.760 Ligands: CLR.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.221, A:I.221, A:L.312, A:L.312, A:W.315, A:L.757, A:L.760 CLR.6: 6 residues within 4Å: Chain A: L.70, V.71, E.74, Y.117, G.120, I.121 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.70, A:V.71, A:Y.117, A:I.121 CLR.7: 5 residues within 4Å: Chain A: Q.856, L.859, L.862, A.863, F.959 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.856, A:Q.856, A:L.859, A:L.862, A:F.959 CLR.8: 8 residues within 4Å: Chain A: A.220, I.221, V.224, L.312, W.315, Y.316 Ligands: CLR.5, CLR.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.220, A:I.221, A:V.224, A:L.312, A:W.315 CLR.9: 8 residues within 4Å: Chain A: I.719, G.723, P.726, A.727, I.730, F.755, L.758, T.845 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.719, A:A.727, A:I.730, A:F.755, A:T.845 CLR.10: 6 residues within 4Å: Chain A: K.213, L.216, V.217, A.220, Y.316 Ligands: CLR.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.217 CLR.11: 4 residues within 4Å: Chain A: W.45, L.49, Y.50, F.135 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.45, A:L.49, A:F.135 CLR.13: 6 residues within 4Å: Chain A: I.59, I.60, A.63, L.70, I.205, T.209 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.59, A:I.60, A:A.63, A:L.70, A:I.205

1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.12: 11 residues within 4Å: Chain A: F.37, F.40, R.41, S.43, K.48, M.51, V.52, T.55, F.193, F.194, I.352 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:M.51, A:V.52, A:F.193, A:F.194, A:I.352 Hydrogen bonds: A:F.40, A:S.43

3 x R0Z: elacridar(Non-covalent)

R0Z.14: 16 residues within 4Å: Chain A: L.65, M.68, M.69, F.336, Q.725, F.728, F.732, E.875, Q.946, M.949, Y.950, Y.953, S.979, F.983, M.986 Ligands: R0Z.16 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.65, A:F.336, A:F.728, A:F.732, A:M.949, A:Y.950, A:F.983, A:F.983, A:F.983 Hydrogen bonds: A:Q.725, A:Y.953 Salt bridges: A:E.875 pi-Stacking: A:F.983 R0Z.15: 14 residues within 4Å: Chain A: W.232, L.236, F.239, I.299, N.721, F.770, Q.773, S.831, A.834, Q.838, Q.990, V.991, F.994 Ligands: R0Z.16 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.232, A:A.834, A:Q.990, A:F.994, A:F.994 Hydrogen bonds: A:N.721, A:Q.773, A:Q.838, A:Q.838 pi-Stacking: A:F.239, A:F.770, A:F.994 R0Z.16: 19 residues within 4Å: Chain A: W.232, A.233, L.236, S.237, F.303, I.306, Y.307, Y.310, L.339, F.343, Q.347, P.350, F.728, M.876, L.879, S.880, F.994 Ligands: R0Z.14, R0Z.15 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.232, A:W.232, A:A.233, A:F.303, A:I.306, A:F.343, A:P.350, A:L.879, A:L.879 Hydrogen bonds: A:Y.310, A:Q.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hamaguchi-Suzuki, N. et al., Cryo-EM structure of P-glycoprotein bound to triple elacridar inhibitor molecules. Biochem.Biophys.Res.Commun. (2024)

Release Date

2024-04-17

Peptides

ATP-dependent translocase ABCB1,mNeonGreen: A
UIC2 Fab light chain: B
UIC2 Fab heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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ATP-dependent translocase ABCB1,mNeonGreen

UIC2 Fab light chain

UIC2 Fab heavy chain

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