SMTL ID : 6zoa.1

Partially induced AcrB T protomer and DDM binding to the TM8/PC2 pathway of AcrB L2 protomer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

hetero-3-2-mer

Ligands

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

LMT.1: 15 residues within 4Å: Chain A: I.38, A.39, S.134, T.463, F.563, E.673, L.674, G.675, D.681, N.719, E.826, G.861, M.862, E.866 Ligands: DDQ.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.38, A:A.39, A:T.463, A:F.563, A:E.866 Hydrogen bonds: A:S.134, A:N.719, A:E.826, A:M.862 LMT.2: 6 residues within 4Å: Chain A: I.27, L.28, V.32, V.341, F.380, I.390 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.27, A:V.341, A:F.380, A:F.380, A:I.390 LMT.3: 10 residues within 4Å: Chain A: G.440, G.444, M.447, V.883, C.887, A.890, L.891 Chain C: R.8, F.11, I.18 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.883, A:A.890, C:I.18 Hydrogen bonds: A:A.890 LMT.4: 4 residues within 4Å: Chain A: R.536, S.537, Y.541, F.1020 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1020 Hydrogen bonds: A:R.536, A:R.536, A:S.537, A:Y.541 LMT.15: 8 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, Y.541, L.544, F.1020 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.544, B:F.1020, B:F.1020 Hydrogen bonds: B:R.536, B:S.537, B:Y.541, B:Y.541 LMT.25: 7 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, R.540, Y.541, F.1020 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.1020 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:S.537, C:Y.541

4 x C14: TETRADECANE(Non-covalent)

C14.5: 7 residues within 4Å: Chain A: A.457, F.458, G.460, G.461, R.468, I.472 Chain C: K.29 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.457, A:F.458, A:F.458, A:I.472 C14.16: 3 residues within 4Å: Chain B: G.296, A.381, A.384 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.384 C14.17: 6 residues within 4Å: Chain B: V.452, Y.467, Y.877, S.880, Q.928, L.932 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.932 C14.18: 5 residues within 4Å: Chain A: R.8, F.11 Chain B: G.440, M.447, L.891 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.891, A:F.11

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

DDQ.6: 12 residues within 4Å: Chain A: Y.35, P.36, T.37, I.38, A.39, P.669, A.670, E.673, A.677, M.862, E.866 Ligands: LMT.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.35, A:P.669, A:P.669 Hydrogen bonds: A:I.38 DDQ.7: 2 residues within 4Å: Chain A: W.515, R.518 No protein-ligand interaction detected (PLIP) DDQ.19: 5 residues within 4Å: Chain B: K.29 Chain C: F.458, F.459, V.883 Ligands: PTY.26 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.458, C:F.458, C:V.883 DDQ.20: 2 residues within 4Å: Chain B: K.510, G.511 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.511 DDQ.28: 3 residues within 4Å: Chain C: M.1, F.4, F.5 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.4, C:F.4, C:F.5 DDQ.29: 6 residues within 4Å: Chain C: E.95, S.96, A.457, F.458, R.468 Ligands: DDQ.30 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.457, C:F.458, C:F.458 Hydrogen bonds: C:S.96 DDQ.30: 5 residues within 4Å: Chain C: F.388, A.457, R.468, S.471 Ligands: DDQ.29 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.457

4 x HEX: HEXANE(Non-covalent)

HEX.8: 1 residues within 4Å: Chain A: M.1 No protein-ligand interaction detected (PLIP) HEX.9: 3 residues within 4Å: Chain A: F.458, I.879 Chain C: L.25 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.25, A:F.458 HEX.21: 1 residues within 4Å: Chain B: F.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.5 HEX.31: 1 residues within 4Å: Chain C: L.480 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.480

1 x D10: DECANE(Non-covalent)

D10.10: 1 residues within 4Å: Chain A: W.895 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.895, A:W.895

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 1 residues within 4Å: Chain A: K.589 Ligand excluded by PLIP

1 x LNK: PENTANE(Non-covalent)

LNK.12: 1 residues within 4Å: Chain A: F.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.5, A:F.5

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain A: N.231, S.233 Chain B: S.84, G.581, N.623, T.724, P.814 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.218, A:S.233, B:S.84, B:G.581, B:N.623, B:T.724, B:T.724 GOL.14: 1 residues within 4Å: Chain A: K.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.29 GOL.23: 4 residues within 4Å: Chain B: E.422, H.505, H.525, R.969 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.525

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

OCT.22: 1 residues within 4Å: Chain B: W.895 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.895, B:W.895 OCT.32: 2 residues within 4Å: Chain C: M.552, F.556 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.556, C:F.556

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

EDO.24: 2 residues within 4Å: Chain B: F.362, R.363 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.362

2 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.26: 14 residues within 4Å: Chain B: F.4, R.8, F.11, I.18 Chain C: Q.439, M.447, C.887, A.890, L.891, Y.892, E.947, K.950, D.951 Ligands: DDQ.19 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.4, B:I.18, C:A.890, C:L.891 Salt bridges: B:R.8 Hydrogen bonds: C:Q.439, C:E.947 PTY.27: 12 residues within 4Å: Chain B: W.13, M.20 Chain C: I.882, F.885, S.894, W.895, S.896, K.950, R.1030, F.1033, S.1034, R.1035 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.882, C:F.885, C:W.895, C:W.895, C:W.895, B:W.13, B:W.13, B:W.13 Hydrogen bonds: C:S.894, C:W.895, C:S.896, C:S.896, C:K.950, C:K.950, C:R.1030 Salt bridges: C:K.950

1 x D12: DODECANE(Non-covalent)

D12.33: 2 residues within 4Å: Chain C: W.13, I.17 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.13, C:W.13, C:I.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tam, H.K. et al., Allosteric drug transport mechanism of multidrug transporter AcrB. Nat Commun (2021)

Release Date

2021-05-19

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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