SMTL ID : 9cup.1

BmrCD in inward-facing conformation bound to Hoechsts

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

26 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 13 residues within 4Å: Chain A: K.16, L.17, I.19, T.20, L.23, L.24, V.27, F.166, L.173, R.180 Ligands: POV.4, POV.9, POV.16 Ligand excluded by PLIP POV.2: 4 residues within 4Å: Chain A: V.268, R.271 Ligands: POV.10, POV.13 Ligand excluded by PLIP POV.3: 11 residues within 4Å: Chain A: K.62, Q.143, P.144, I.146, K.147, V.150, I.153, C.154, G.157 Chain B: F.288 Ligands: POV.20 Ligand excluded by PLIP POV.4: 16 residues within 4Å: Chain A: V.27, G.30, A.31, T.34, F.37, I.38, K.41, D.45, H.46, R.77, L.152, L.155, L.159, T.243, L.247 Ligands: POV.1 Ligand excluded by PLIP POV.5: 13 residues within 4Å: Chain A: K.251, L.252, V.255, A.258, I.259, I.262, I.344, L.347, A.348, C.351, W.354, H.355, F.383 Ligand excluded by PLIP POV.6: 9 residues within 4Å: Chain A: K.2, I.3, G.4, L.7, L.223, V.227, L.396, R.400 Ligands: POV.11 Ligand excluded by PLIP POV.7: 15 residues within 4Å: Chain A: I.262, L.265, W.266, I.269, Y.273, Y.277, R.328, N.331, L.335, M.336, L.340, V.343, I.344 Chain B: Y.94 Ligands: POV.25 Ligand excluded by PLIP POV.8: 8 residues within 4Å: Chain A: F.239, F.242, T.243, F.246, L.247, V.250, L.257, V.260 Ligand excluded by PLIP POV.9: 22 residues within 4Å: Chain A: L.24, V.164, F.165, Y.168, G.169, Y.172, L.173 Chain B: V.193, A.197, Y.201, R.208, M.258, K.259, F.262, L.266, P.269, T.270, L.273, L.274 Ligands: POV.1, POV.16, POV.17 Ligand excluded by PLIP POV.10: 14 residues within 4Å: Chain A: F.231, S.234, G.235, M.238, V.260, I.263, W.264, S.267, V.268, R.271, I.389, F.393, L.396 Ligands: POV.2 Ligand excluded by PLIP POV.11: 17 residues within 4Å: Chain A: G.4, L.7, W.8, A.11, L.12, R.15, L.18, I.19, V.22, L.23, L.223, Y.224, V.227, L.228, V.232 Ligands: POV.6, POV.12 Ligand excluded by PLIP POV.12: 5 residues within 4Å: Chain A: G.4, K.5, W.8, L.12 Ligands: POV.11 Ligand excluded by PLIP POV.13: 2 residues within 4Å: Chain A: R.272 Ligands: POV.2 Ligand excluded by PLIP POV.16: 9 residues within 4Å: Chain A: Y.172, M.176, R.180, Q.183 Chain B: Y.254, Q.255, M.258 Ligands: POV.1, POV.9 Ligand excluded by PLIP POV.17: 7 residues within 4Å: Chain B: Y.201, K.204, R.208, F.262, I.263, L.266 Ligands: POV.9 Ligand excluded by PLIP POV.18: 11 residues within 4Å: Chain B: S.199, G.202, S.203, H.206, E.207, T.210, I.321, N.322, Q.325, R.326 Ligands: POV.28 Ligand excluded by PLIP POV.19: 9 residues within 4Å: Chain B: L.39, T.42, I.43, V.46, L.47, A.50, M.96 Ligands: POV.22, POV.24 Ligand excluded by PLIP POV.20: 14 residues within 4Å: Chain A: I.153, G.157, L.160 Chain B: A.186, I.189, P.190, A.277, L.280, I.281, G.284, Y.285, F.288, R.292 Ligands: POV.3 Ligand excluded by PLIP POV.21: 8 residues within 4Å: Chain B: A.76, E.77, L.80, F.81, G.84, I.85, V.88 Ligands: POV.22 Ligand excluded by PLIP POV.22: 15 residues within 4Å: Chain B: A.50, V.53, I.54, F.57, L.61, N.64, D.68, F.81, Y.82, I.85, L.89, M.96 Ligands: POV.19, POV.21, POV.23 Ligand excluded by PLIP POV.23: 13 residues within 4Å: Chain B: L.49, A.50, V.53, F.57, K.60, M.166, M.169, T.170, L.173, T.174, F.177, L.178 Ligands: POV.22 Ligand excluded by PLIP POV.24: 9 residues within 4Å: Chain B: I.43, L.47, V.88, A.92, I.95, M.96, F.99 Ligands: POV.19, POV.25 Ligand excluded by PLIP POV.25: 17 residues within 4Å: Chain A: N.327, R.328, N.331, L.335, V.343 Chain B: F.87, V.88, T.90, A.91, A.92, Y.94, I.95, Y.98, F.99, H.102 Ligands: POV.7, POV.24 Ligand excluded by PLIP POV.26: 12 residues within 4Å: Chain B: L.27, K.28, G.31, F.34, K.35, W.38, Y.41, T.42, I.45, V.46, I.158, L.161 Ligand excluded by PLIP POV.27: 8 residues within 4Å: Chain B: M.169, F.172, L.173, S.180, W.181, K.182, F.185, E.294 Ligand excluded by PLIP POV.28: 12 residues within 4Å: Chain B: M.168, F.172, I.188, P.192, A.195, I.196, S.199, M.310, M.314, I.317, I.321 Ligands: POV.18 Ligand excluded by PLIP

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

ATP.14: 18 residues within 4Å: Chain A: D.202, N.203, Y.439, Q.440, E.443, V.445, G.466, S.467, G.468, K.469, S.470, S.471, Y.480, Q.511, D.591, E.592, I.621 Ligands: MG.15 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:E.443, A:E.443, A:G.466, A:S.467, A:G.468, A:K.469, A:S.470, A:S.471, A:S.471, A:E.592 Salt bridges: A:K.469, A:K.469 pi-Stacking: A:Y.439, A:Y.439 ATP.29: 16 residues within 4Å: Chain B: E.132, Y.368, P.369, S.370, S.371, N.375, K.394, T.395, G.396, S.397, G.398, K.399, T.400, T.401, Q.441, D.522 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:E.132, B:S.371, B:N.375, B:G.396, B:S.397, B:G.398, B:K.399, B:T.400, B:T.400, B:T.400, B:T.401, B:Q.441, B:Q.441, B:D.522 Salt bridges: B:K.399, B:K.399

1 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 4 residues within 4Å: Chain A: K.469, E.592, H.623 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.592

2 x HT1: 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE(Non-covalent)

HT1.30: 16 residues within 4Å: Chain A: Q.326, N.333, H.338, R.345, Q.384 Chain B: M.101, F.105, A.108, E.112, Q.148, S.151, L.152, F.156, L.159, W.312 Ligands: HT1.31 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.105, B:F.105, B:L.152, B:F.156 Hydrogen bonds: B:L.152 HT1.31: 18 residues within 4Å: Chain A: A.31, E.32, G.35, P.36, Y.156, L.160, Y.237, R.381, Q.384 Chain B: K.272, V.275, G.276, Y.279, I.311, W.312, F.315, E.319 Ligands: HT1.30 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:K.272, B:V.275, B:Y.279, B:Y.279, B:I.311, B:W.312, B:W.312, A:Y.156, A:L.160, A:Q.384 Salt bridges: B:E.319 pi-Stacking: B:F.315 Hydrogen bonds: A:R.381

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, Q. et al., Lipid-mediated mechanism of drug extrusion by a heterodimeric ABC exporter. Biorxiv (2025)

Release Date

2025-08-13

Peptides

Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH: A
Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

Membrane

We predict this structure to be a membrane protein.
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Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH

Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI

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