SMTL ID : 8t3k.1

Heterodimeric ABC transporter BmrCD in the inward-facing conformation bound to ATP: BmrCD_IF-ATP2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

POV.1: 10 residues within 4Å: Chain A: T.34, F.37, I.38, K.41, L.152, L.155, T.243, A.244, L.247 Ligands: POV.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.37, A:F.37, A:F.37, A:L.152, A:L.155, A:L.247 Hydrogen bonds: A:K.41 Salt bridges: A:K.41 POV.2: 9 residues within 4Å: Chain A: M.238, F.239, F.242, T.243, F.246, V.250, K.251, F.254, L.257 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.239, A:F.242, A:F.246, A:F.246, A:F.246, A:F.246, A:F.246, A:V.250, A:F.254, A:L.257 Salt bridges: A:K.251 POV.3: 7 residues within 4Å: Chain A: L.151, A.154, L.155, G.158, L.159, F.162 Ligands: POV.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.155, A:L.159 POV.4: 6 residues within 4Å: Chain A: W.8, L.12, R.15, K.16, I.19, L.23 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.15 POV.5: 14 residues within 4Å: Chain A: K.2, I.3, G.4, K.5, L.7, W.8, A.11, L.223, Y.224, V.227, L.228, L.396, R.400 Ligands: POV.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.8, A:W.8, A:L.223, A:Y.224, A:V.227, A:L.228, A:L.396 Hydrogen bonds: A:I.3, A:G.4 Salt bridges: A:K.2, A:K.2, A:K.5 POV.6: 4 residues within 4Å: Chain A: K.5, W.8, R.9 Ligands: POV.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.8 POV.7: 9 residues within 4Å: Chain A: L.24, F.165, F.166, Y.168, G.169, Y.172, L.173, M.176 Chain B: F.262 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.24, A:Y.168, A:Y.172 POV.9: 5 residues within 4Å: Chain B: S.180, W.181, K.182, F.185 Ligands: POV.12 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.181, B:W.181 Salt bridges: B:K.182 POV.10: 9 residues within 4Å: Chain B: V.53, M.56, F.57, K.60, L.61, N.64, T.174, L.178, Y.306 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.53, B:F.57, B:K.60, B:K.60 POV.11: 6 residues within 4Å: Chain A: I.153 Chain B: L.280, I.281, G.284, Y.285, F.288 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.280, B:L.280, B:I.281, B:Y.285, B:F.288, B:F.288 POV.12: 6 residues within 4Å: Chain B: W.181, K.182, F.185, A.186, Y.285 Ligands: POV.9 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.182, B:F.185, B:A.186 Salt bridges: B:K.182 POV.13: 4 residues within 4Å: Chain B: I.196, L.200, S.203, K.204 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.200 Hydrogen bonds: B:S.203 Salt bridges: B:K.204, B:K.204 POV.14: 4 residues within 4Å: Chain B: W.32, K.35, A.36, W.38 No protein-ligand interaction detected (PLIP)

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

ATP.8: 14 residues within 4Å: Chain A: D.202, N.203, Y.439, Q.440, V.445, H.464, T.465, G.466, S.467, G.468, K.469, S.470, S.471, Y.480 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.466, A:S.467, A:G.468, A:K.469, A:S.470, 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.15: 14 residues within 4Å: Chain B: Y.368, N.375, K.394, T.395, G.396, S.397, G.398, K.399, T.400, T.401, Q.441, D.521, Q.522, L.551 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.375, B:G.396, B:S.397, B:K.399, B:T.400, B:T.400, B:Q.441, B:Q.441, B:Q.522, B:Q.522 pi-Stacking: B:Y.368, B:Y.368

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

2023-11-29

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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