SMTL ID : 9hci.1

structure of the double Cys-substituted cross-linked AcrB variant S562C_T837C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-3-2-mer

Ligands

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

LMT.1: 11 residues within 4Å: Chain A: I.27, L.28, K.29, L.30, V.32, V.341, L.344, I.348, L.377, F.380 Ligands: LMT.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.27, A:I.27, A:V.341, A:I.348, A:L.377, A:F.380 Hydrogen bonds: A:K.29 Water bridges: A:L.28 LMT.2: 17 residues within 4Å: Chain A: T.463, Y.467, F.556, S.561, F.563, G.870, N.871, A.873, Y.877, S.880, L.881, V.905, N.923, Q.928, L.931, L.932, I.935 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.877, A:Y.877, A:L.881, A:V.905, A:L.931, A:L.932, A:I.935, A:I.935 Hydrogen bonds: A:S.561, A:N.923, A:Q.928 LMT.3: 8 residues within 4Å: Chain A: G.440, G.444, C.887, A.890, L.891 Chain C: R.8, F.11, I.18 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:F.11, C:I.18, A:A.890 Hydrogen bonds: C:R.8, C:R.8, A:G.440, A:G.444 Water bridges: A:A.890 LMT.5: 9 residues within 4Å: Chain A: I.335, H.338, E.339, K.342, V.345, E.346, I.349, D.633, A.635 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.346, A:I.349 Hydrogen bonds: A:D.633, A:A.635 Salt bridges: A:K.342 LMT.9: 12 residues within 4Å: Chain A: L.28, K.29 Chain B: S.450, A.451, V.454, F.458, N.871, Q.872, S.875, L.876, I.879 Ligands: LMT.1 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Salt bridges: A:K.29 Hydrophobic interactions: B:V.454, B:F.458, B:L.876, B:I.879, B:I.879 Hydrogen bonds: B:N.871, B:N.871, B:S.875 LMT.18: 9 residues within 4Å: Chain B: S.530, G.533, R.536, S.537, R.540, Y.541, L.976, I.1019, F.1020 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.976, B:I.1019, B:F.1020, B:F.1020 Hydrogen bonds: B:R.536, B:R.536, B:S.537, B:R.540, B:Y.541 LMT.23: 13 residues within 4Å: Chain B: F.459, Y.467, F.556, E.866, S.869, G.870, A.873, Y.877, L.881, V.905, N.923, Q.928, L.932 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.877, B:L.881, B:V.905, B:L.932 Hydrogen bonds: B:Y.467, B:E.866, B:Y.877, B:N.923 LMT.28: 8 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, R.540, Y.541, F.1020 Ligands: D10.41 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:R.540, C:Y.541

9 x D10: DECANE(Non-covalent)(Non-functional Binders)

D10.4: 2 residues within 4Å: Chain A: W.13 Ligands: D10.19 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.13, A:W.13, A:W.13 D10.12: 3 residues within 4Å: Chain B: A.457, F.458, I.472 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.457, B:F.458, B:I.472 D10.14: 3 residues within 4Å: Chain B: M.1, N.3, Q.439 No protein-ligand interaction detected (PLIP) D10.19: 4 residues within 4Å: Chain B: I.882, W.895 Ligands: D10.4, D12.20 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.882, B:W.895 D10.21: 3 residues within 4Å: Chain B: I.27, D.301, I.337 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.27, B:I.337 D10.32: 3 residues within 4Å: Chain C: M.1, F.4, F.5 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.4, C:F.5 D10.34: 3 residues within 4Å: Chain B: A.22, L.25 Chain C: F.458 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.458, C:F.458, B:A.22, B:L.25 D10.41: 3 residues within 4Å: Chain C: S.523, Y.527 Ligands: LMT.28 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.527 D10.42: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: P.50, R.185, E.273, N.274, G.755, G.756, Y.772, M.774 Ligand excluded by PLIP GOL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain B: R.239, N.760, D.761 Chain C: P.119, Q.120, E.121 Ligand excluded by PLIP GOL.11: 8 residues within 4Å: Chain A: Q.218, N.231, S.233 Chain B: S.84, G.581, N.623, T.724, P.814 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain B: R.699, N.700, L.703, P.718 Ligand excluded by PLIP GOL.15: 9 residues within 4Å: Chain B: P.50, R.185, E.273, N.274, G.755, G.756, S.757, Y.772, M.774 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: R.168, E.309 Chain B: L.75, M.76, Y.77, M.78, N.820 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain B: L.111, Q.112, M.115, G.126, V.127 Chain C: Q.112, P.116 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain B: F.727, I.729, P.783, I.786, S.802, S.805, S.806, S.807 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain B: Q.218, N.231, A.232, S.233 Chain C: S.84, T.724 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain A: G.581, T.724, P.814 Chain C: Q.218, N.231, S.233 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain C: D.566, E.567, D.568, K.643, S.997, G.998 Ligand excluded by PLIP GOL.39: 7 residues within 4Å: Chain C: R.185, E.273, N.274, G.755, G.756, Y.772, M.774 Ligand excluded by PLIP GOL.43: 4 residues within 4Å: Chain B: N.700 Chain D: R.23, W.57, H.59 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain D: N.122, D.143, F.145, K.147, I.152 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain B: Y.811 Chain D: E.20, R.23, D.44, L.53 Ligand excluded by PLIP

4 x D12: DODECANE(Non-covalent)

D12.7: 6 residues within 4Å: Chain A: F.11 Chain B: G.440, G.444, M.447, A.890, L.891 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.890, A:F.11, A:F.11, A:F.11 D12.20: 5 residues within 4Å: Chain B: F.885, S.896, F.899, F.1033 Ligands: D10.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.885, B:F.899 D12.30: 2 residues within 4Å: Chain C: W.13, I.17 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.17 D12.33: 3 residues within 4Å: Chain C: V.454, F.458, F.459 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.454, C:F.459

3 x HEX: HEXANE(Non-covalent)(Non-functional Binders)

HEX.22: 1 residues within 4Å: Chain B: F.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.4, B:F.4 HEX.35: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.37: 3 residues within 4Å: Chain C: F.380, I.390, M.395 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.380, C:I.390

1 x C14: TETRADECANE(Non-covalent)

C14.26: 3 residues within 4Å: Chain B: W.13, I.17 Chain C: W.895 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.13, B:W.13, B:W.13, B:I.17

2 x OCT: N-OCTANE(Non-covalent)

OCT.29: 2 residues within 4Å: Chain C: W.895 Ligands: OCT.31 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.895, C:W.895 OCT.31: 5 residues within 4Å: Chain C: S.894, W.895, S.896, R.1030 Ligands: OCT.29 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.895

1 x DD9: nonane(Non-covalent)

DD9.36: 3 residues within 4Å: Chain C: F.388, A.457, R.468 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.388, C:A.457

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

SO4.40: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boernsen, C. et al., Molecular mechanism of transition-state inhibitors of bacterial antibiotic efflux pumps. To Be Published

Release Date

2025-11-19

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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