SMTL ID : 8avy.1

The ABCB1 L335C mutant (mABCB1) in the Apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 23 residues within 4Å: Chain A: D.160, Y.397, S.399, R.400, I.405, S.425, G.426, G.427, G.428, K.429, S.430, T.431, Q.471, H.583, R.901, T.1170, Q.1171, L.1172, S.1173, G.1174, G.1175, Q.1176 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:D.160, A:S.399, A:R.400, A:R.400, A:G.426, A:G.427, A:G.428, A:K.429, A:S.430, A:T.431, A:T.431, A:Y.440, A:Q.471, A:E.552, A:E.552, A:R.901, A:S.1173, A:G.1174, A:G.1175, A:Q.1176, A:Q.1176 Salt bridges: A:K.429, A:K.429, A:H.583 pi-Stacking: A:Y.397, A:Y.397 ATP.3: 21 residues within 4Å: Chain A: A.525, Q.526, L.527, S.528, G.529, G.530, Q.531, D.801, Y.1040, T.1042, R.1043, S.1068, G.1069, G.1070, G.1071, K.1072, S.1073, T.1074, Y.1083, Q.1114 Ligands: MG.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.528, A:G.529, A:G.530, A:Q.531, A:Q.531, A:D.801, A:R.1043, A:G.1069, A:G.1069, A:G.1070, A:G.1071, A:G.1071, A:K.1072, A:S.1073, A:S.1073, A:T.1074, A:T.1074, A:Q.1114 Salt bridges: A:K.1072, A:K.1072 pi-Stacking: A:Y.1040, A:Y.1040

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.430, Q.471, D.551 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.430, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain A: S.1073, Q.1114 Ligands: ATP.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.1073, H2O.1, H2O.1

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.5: 15 residues within 4Å: Chain A: L.36, F.39, R.40, R.47, M.50, W.132, I.186, F.189, F.190, N.347, I.348, F.351 Ligands: Y01.9, Y01.10, Y01.11 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.36, A:F.39, A:F.39, A:W.132, A:I.186, A:F.189, A:F.190, A:I.348, A:F.351, A:F.351 Y01.6: 8 residues within 4Å: Chain A: Y.49, Y.126, F.131, L.134, Y.924, M.928, H.932 Ligands: Y01.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.126, A:F.131, A:L.134 Hydrogen bonds: A:Y.924 Salt bridges: A:H.932 Y01.7: 6 residues within 4Å: Chain A: T.108, Y.112, T.115, F.947, R.954 Ligands: Y01.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.112, A:F.947, A:F.947, A:F.947, A:F.947, A:F.947, A:R.954, A:R.954 Salt bridges: A:R.954 Y01.8: 6 residues within 4Å: Chain A: L.856, I.860, M.944, A.951, R.954 Ligands: Y01.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.856, A:I.860, A:A.951 Salt bridges: A:R.954 Y01.9: 7 residues within 4Å: Chain A: L.36, I.58, M.193, F.197 Ligands: Y01.5, Y01.10, Y01.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.58, A:M.193, A:F.197 Y01.10: 13 residues within 4Å: Chain A: V.35, F.189, M.193, L.221, G.222, A.225, A.229, K.230, I.348, R.355, Y.359 Ligands: Y01.5, Y01.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.189, A:L.221, A:A.225, A:A.229, A:I.348, A:I.348 Hydrogen bonds: A:Y.359, A:Y.359 Salt bridges: A:K.230 Y01.11: 6 residues within 4Å: Chain A: L.36, T.54, I.58, F.190 Ligands: Y01.5, Y01.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.54 Y01.12: 10 residues within 4Å: Chain A: W.44, L.45, L.48, Y.49, V.52, I.59, V.124, I.127, F.131 Ligands: Y01.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.45, A:L.45, A:L.48, A:Y.49, A:I.59, A:V.124, A:I.127, A:F.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gewering, T. et al., Tracing the substrate translocation mechanism in P-glycoprotein. Elife (2024)

Release Date

2023-09-06

Peptides

ATP-dependent translocase ABCB1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

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

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