SMTL ID : 8fmv.1

Heterodimeric ABC transporter BmrCD in the inward-facing conformation bound to substrate and ATP: BmrCD_IF-2HT/ATP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

POV.1: 15 residues within 4Å: Chain A: K.16, L.17, T.20, L.23, L.24, V.27, F.162, F.166, Y.168, G.169, Y.172, L.173, M.176 Chain B: F.262 Ligands: POV.9 Ligand excluded by PLIP POV.2: 12 residues within 4Å: Chain A: K.2, I.3, G.4, K.5, L.7, W.8, L.223, V.227, L.396, R.400 Ligands: POV.7, POV.8 Ligand excluded by PLIP POV.3: 15 residues within 4Å: Chain A: I.269, Y.273, Y.277, R.328, N.331, L.332, L.335, M.336, L.340 Chain B: Y.94, I.95, Y.98, F.99 Ligands: POV.5, POV.18 Ligand excluded by PLIP POV.4: 12 residues within 4Å: Chain A: G.235, M.238, F.239, F.242, T.243, F.246, L.247, V.250, L.257, V.260 Ligands: POV.8, POV.10 Ligand excluded by PLIP POV.5: 5 residues within 4Å: Chain A: I.269, R.272, Y.273, Y.276 Ligands: POV.3 Ligand excluded by PLIP POV.6: 14 residues within 4Å: Chain A: T.26, V.29, G.30, L.33, T.34, F.37, I.38, I.236, F.239, G.240, T.243, A.244, L.247, Y.378 Ligand excluded by PLIP POV.7: 17 residues within 4Å: Chain A: G.4, K.5, L.7, W.8, A.11, L.12, R.15, L.18, I.19, V.22, L.223, Y.224, V.227, L.228, V.232 Ligands: POV.2, POV.8 Ligand excluded by PLIP POV.8: 18 residues within 4Å: Chain A: V.227, F.231, V.232, S.234, G.235, I.236, M.238, F.239, F.242, V.260, I.263, R.271, I.389, F.393, L.396 Ligands: POV.2, POV.4, POV.7 Ligand excluded by PLIP POV.9: 12 residues within 4Å: Chain A: F.162, V.164, F.165, F.166, Y.168 Chain B: Y.201, F.262, L.266, P.269, T.270, L.273 Ligands: POV.1 Ligand excluded by PLIP POV.10: 5 residues within 4Å: Chain A: F.246, V.250, F.254, L.257 Ligands: POV.4 Ligand excluded by PLIP POV.11: 11 residues within 4Å: Chain A: I.146, K.147, V.150, I.153, A.154, L.155, G.157, G.158, L.159 Chain B: L.280 Ligands: POV.17 Ligand excluded by PLIP POV.12: 19 residues within 4Å: Chain A: V.255, A.256, I.259, I.344, L.347, A.348, V.350, A.351, W.354, L.379, F.383 Chain B: F.81, I.83, G.84, I.85, F.87, V.88, A.91 Ligands: POV.18 Ligand excluded by PLIP POV.15: 10 residues within 4Å: Chain B: F.172, L.173, G.176, I.179, S.180, W.181, K.182, F.185, E.294 Ligands: POV.22 Ligand excluded by PLIP POV.16: 13 residues within 4Å: Chain B: V.53, M.56, F.57, K.60, L.61, N.64, F.81, T.170, L.173, T.174, F.177, L.178 Ligands: POV.22 Ligand excluded by PLIP POV.17: 12 residues within 4Å: Chain A: I.153 Chain B: A.186, I.189, P.190, A.277, L.280, I.281, G.284, Y.285, F.288, R.292 Ligands: POV.11 Ligand excluded by PLIP POV.18: 13 residues within 4Å: Chain B: R.40, I.43, L.47, V.88, A.91, A.92, I.95, M.96, F.99, H.102, Q.103 Ligands: POV.3, POV.12 Ligand excluded by PLIP POV.19: 16 residues within 4Å: Chain B: L.27, K.28, G.31, W.32, F.34, K.35, W.38, Y.41, T.42, I.45, L.49, I.158, L.161, V.162, T.165, M.166 Ligand excluded by PLIP POV.20: 9 residues within 4Å: Chain B: M.168, P.192, A.195, I.196, S.199, S.203, M.314, I.317, I.321 Ligand excluded by PLIP POV.21: 7 residues within 4Å: Chain B: L.200, Y.201, K.204, R.208, F.262, I.263, L.266 Ligand excluded by PLIP POV.22: 9 residues within 4Å: Chain B: F.177, L.178, I.179, S.180, E.294, L.295, E.299 Ligands: POV.15, POV.16 Ligand excluded by PLIP

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

ATP.13: 14 residues within 4Å: Chain A: D.202, N.203, Y.439, Q.440, V.445, T.465, G.466, S.467, G.468, K.469, S.470, S.471, Y.480 Ligands: MG.14 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.202, A:G.466, A:G.466, A:S.467, A:G.468, A:K.469, A:S.470, A:S.470, A:S.471 Salt bridges: A:K.469, A:K.469 pi-Stacking: A:Y.439, A:Y.439 ATP.23: 18 residues within 4Å: Chain B: E.132, Y.368, S.370, S.371, S.373, N.375, K.394, T.395, G.396, S.397, G.398, K.399, T.400, T.401, Q.441, D.521, Q.522, H.553 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:E.132, B:S.371, B:N.375, B:G.396, B:G.398, B:K.399, B:T.400, B:T.401, B:Q.441, B:Q.441, B:Q.441, B:Q.522

1 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 3 residues within 4Å: Chain A: K.469, S.470 Ligands: ATP.13 No protein-ligand interaction detected (PLIP)

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

HT1.24: 16 residues within 4Å: Chain A: H.338, R.345, D.377, N.380, R.381, Q.384 Chain B: F.105, L.152, F.156, L.159, Y.279, G.308, M.309, I.311, W.312 Ligands: HT1.25 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.105, B:L.152, B:F.156, B:F.156, B:L.159, B:I.311 Hydrogen bonds: B:Y.279, A:H.338, A:Q.384 pi-Stacking: B:W.312, B:W.312, B:W.312 pi-Cation interactions: A:H.338 HT1.25: 21 residues within 4Å: Chain A: E.32, Y.237, D.377, R.381, Q.384 Chain B: I.198, G.202, I.205, H.206, F.209, D.264, F.267, E.268, V.271, K.272, V.275, G.276, Y.279, I.311, F.315 Ligands: HT1.24 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.271, B:V.275, B:Y.279, B:I.311, B:F.315 Hydrogen bonds: B:Y.279 pi-Stacking: B:F.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, Q. et al., Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. Nat Commun (2023)

Release Date

2023-11-15

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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