SMTL ID : 7oul.1

BDM88832 inhibitor bound to the transmembrane domain of AcrB-R971A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-2-mer

Ligands

6 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.1: 9 residues within 4Å: Chain A: I.27, L.28, K.29, V.32, H.338, V.341, P.373, F.380 Ligands: LMT.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.27, A:I.27, A:V.32, A:V.341, A:V.341, A:F.380 LMT.2: 10 residues within 4Å: Chain A: G.440, A.441, G.444, M.447, C.887, A.890, L.891 Chain C: R.8, F.11, I.18 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.11, C:I.18, A:M.447, A:A.890 Hydrogen bonds: C:R.8, A:G.440 Salt bridges: C:R.8 LMT.6: 9 residues within 4Å: Chain A: I.335, H.338, E.339, V.341, V.345, E.346, D.633, W.634, A.635 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.341, A:V.345, A:E.346 Hydrogen bonds: A:E.339, A:D.633 LMT.9: 9 residues within 4Å: Chain A: L.25, K.29 Chain B: S.450, F.458, N.871, Q.872, S.875, I.879 Ligands: LMT.1 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Salt bridges: A:K.29 Hydrophobic interactions: B:F.458, B:F.458, B:I.879 Hydrogen bonds: B:N.871, B:Q.872, B:S.875 LMT.10: 9 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.1017, F.1020 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.534, B:L.1017, B:F.1020 Hydrogen bonds: B:R.536, B:S.537, B:S.537, B:Y.541 LMT.19: 8 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, R.540, Y.541, L.1017, F.1020 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.1017, C:F.1020, C:F.1020 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:R.540, C:R.540, C:Y.541

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: P.50, R.185, E.273, G.755, Y.772, M.774 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.185, A:R.185 EDO.8: 4 residues within 4Å: Chain A: N.231, S.233 Chain B: S.84, T.724 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.724, B:T.724 EDO.13: 4 residues within 4Å: Chain B: Q.228, Q.229, L.230 Chain C: L.782 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.228, B:Q.229, B:L.230 Water bridges: B:L.230 EDO.14: 4 residues within 4Å: Chain B: N.189, R.263, D.264, K.267 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.189 EDO.15: 7 residues within 4Å: Chain B: F.727, I.729, P.783, I.786, S.802, S.805, S.807 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.783, B:S.805, B:S.807 EDO.16: 4 residues within 4Å: Chain B: Q.218, N.231, S.233 Chain C: S.84 No protein-ligand interaction detected (PLIP) EDO.17: 6 residues within 4Å: Chain A: S.84, G.581, T.724 Chain C: Q.218, N.231, S.233 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.581, A:T.724, A:T.724, C:Q.218, C:N.231 EDO.23: 1 residues within 4Å: Chain C: W.809 No protein-ligand interaction detected (PLIP) EDO.25: 4 residues within 4Å: Chain B: Y.811 Chain D: E.20, R.23, D.44 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.811, D:R.23 EDO.26: 5 residues within 4Å: Chain B: E.693 Chain D: Y.56, W.57, F.90, H.92 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.92 EDO.27: 4 residues within 4Å: Chain A: Y.811 Chain E: E.20, R.23, D.44 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:Y.811, E:R.23, E:D.44

1 x 1KE: 1-(3-chloranyl-5-iodanyl-pyridin-2-yl)piperazine(Non-covalent)

1KE.4: 9 residues within 4Å: Chain A: L.404, D.407, D.408, V.411, L.442, I.445, A.446, L.449, K.940 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.445 Hydrogen bonds: A:D.408

1 x D12: DODECANE(Non-covalent)

D12.5: 6 residues within 4Å: Chain A: F.386, F.458, R.468, I.472, V.475, S.476 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.386, A:F.458, A:I.472, A:V.475

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: K.55, G.691, H.692, E.693 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.692 Salt bridges: A:K.55 SO4.11: 4 residues within 4Å: Chain B: N.361, F.362, R.363, K.498 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.362, B:R.363 Salt bridges: B:K.498 SO4.24: 3 residues within 4Å: Chain C: K.55, G.691, H.692 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.692 Salt bridges: C:K.55

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 7 residues within 4Å: Chain A: R.168, T.169 Chain B: L.75, M.76, Y.77, M.78, N.820 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.75, B:M.78, A:R.168, A:E.309 GOL.22: 7 residues within 4Å: Chain A: G.51, W.754, G.755, M.774 Chain C: Q.218, G.221, T.222 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.222, A:W.754 Water bridges: C:Q.218, C:T.222

1 x LPX: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate(Non-covalent)

LPX.18: 8 residues within 4Å: Chain B: I.17 Chain C: I.882, F.885, E.893, S.894, W.895, S.896, F.1033 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.882, C:F.885, C:W.895, C:W.895, B:I.17 Hydrogen bonds: C:W.895, C:S.896, C:S.896, C:S.896

1 x DDQ: DECYLAMINE-N,N-DIMETHYL-N-OXIDE(Non-covalent)

DDQ.20: 2 residues within 4Å: Chain C: F.4, F.5 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.4, C:F.5

1 x C14: TETRADECANE(Non-covalent)

C14.21: 2 residues within 4Å: Chain C: F.458, N.871 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.458, C:N.871

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ple, C. et al., Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps. Nat Commun (2022)

Release Date

2021-12-29

Peptides

Multidrug efflux pump subunit AcrB: ABC
DARPIN: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Multidrug efflux pump subunit AcrB

DARPIN

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