SMTL ID : 6bpl.1

E. coli MsbA in complex with LPS and inhibitor G907

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

homo-dimer

Ligands

1 x GMH- GLC- GLC- GLC- GMH: alpha-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero-alpha-D-manno-heptopyranose-(1-7)]L-glycero-alpha-D-manno-heptopyranose

GMH-GLC-GLC-GLC-GMH.1: 6 residues within 4Å: Chain A: S.86, Y.130, R.310 Ligands: GCS-KDO-KDO-GMH.2, GCS-KDO-KDO-GMH.2, DPO.18 No protein-ligand interaction detected (PLIP)

1 x GCS- KDO- KDO- GMH: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-[L-glycero-alpha-D-manno-heptopyranose-(1-5)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose

GCS-KDO-KDO-GMH.2: 12 residues within 4Å: Chain A: R.296 Chain B: R.296, K.299, S.300 Ligands: GMH-GLC-GLC-GLC-GMH.1, GMH-GLC-GLC-GLC-GMH.1, PA1.10, FTT.13, FTT.15, MYR.16, PO4.17, DPO.18 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.299

4 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.3: 5 residues within 4Å: Chain A: T.42, F.43, M.159, Y.162, Y.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.163 3PE.6: 4 residues within 4Å: Chain B: F.43, S.46, M.159, Y.162 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.43 Hydrogen bonds: B:S.46, B:Y.162 3PE.7: 1 residues within 4Å: Chain B: Y.83 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.83 3PE.8: 2 residues within 4Å: Chain B: R.14, W.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.17

2 x AU7: (2E)-3-{6-[(1S)-1-(2-chloro-6-cyclopropylphenyl)ethoxy]-4-cyclopropylquinolin-3-yl}prop-2-enoic acid(Non-covalent)

AU7.4: 16 residues within 4Å: Chain A: F.157, L.171, A.175, V.178, S.179, I.182, R.190, I.255, A.259, A.262, L.263, M.291, L.294, M.295, L.298, K.299 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.157, A:L.171, A:L.171, A:L.171, A:A.175, A:V.178, A:I.182, A:I.182, A:A.259, A:A.262, A:L.294, A:L.294, A:M.295, A:L.298, A:L.298 Salt bridges: A:R.190, A:K.299 Halogen bonds: A:A.259 AU7.9: 15 residues within 4Å: Chain B: F.157, L.171, I.172, A.175, V.178, S.179, I.182, I.255, A.259, M.291, L.294, M.295, L.298, K.299, T.302 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.157, B:L.171, B:I.172, B:A.175, B:V.178, B:V.178, B:I.182, B:I.182, B:L.294, B:L.298 Salt bridges: B:K.299 Halogen bonds: B:A.259

4 x FTT: 3-HYDROXY-TETRADECANOIC ACID(Non-covalent)

FTT.5: 11 residues within 4Å: Chain A: L.263, F.288, M.295, R.296 Chain B: V.71, M.75, R.78 Ligands: PA1.10, PO4.11, FTT.12, DAO.14 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.263, A:F.288, B:V.71 Hydrogen bonds: A:R.296 FTT.12: 8 residues within 4Å: Chain B: M.44, L.45, M.67 Ligands: FTT.5, PA1.10, PO4.11, FTT.13, DAO.14 No protein-ligand interaction detected (PLIP) FTT.13: 8 residues within 4Å: Chain A: L.45, I.292, A.293 Ligands: GCS-KDO-KDO-GMH.2, FTT.12, DAO.14, FTT.15, MYR.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.45, A:I.292, A:A.293 FTT.15: 7 residues within 4Å: Chain A: M.44, L.47, L.48, R.78 Ligands: GCS-KDO-KDO-GMH.2, FTT.13, MYR.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.47

1 x PA1: 2-amino-2-deoxy-alpha-D-glucopyranose(Non-covalent)

PA1.10: 8 residues within 4Å: Chain A: R.296 Chain B: R.78, R.296 Ligands: GCS-KDO-KDO-GMH.2, GCS-KDO-KDO-GMH.2, FTT.5, PO4.11, FTT.12 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.296, B:R.78 Salt bridges: A:R.296, B:R.296

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 4 residues within 4Å: Chain B: R.78 Ligands: FTT.5, PA1.10, FTT.12 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.78 PO4.17: 4 residues within 4Å: Chain A: R.78 Chain B: Q.256 Ligands: GCS-KDO-KDO-GMH.2, MYR.16 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.256 Salt bridges: A:R.78

1 x DAO: LAURIC ACID(Non-covalent)

DAO.14: 10 residues within 4Å: Chain A: T.285, F.288, S.289 Chain B: L.48, S.289, I.292, A.293 Ligands: FTT.5, FTT.12, FTT.13 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.285, A:F.288, B:L.48, B:I.292

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.16: 13 residues within 4Å: Chain A: V.71, M.75, R.78 Chain B: Q.256, S.260, L.263, L.267, F.288, M.295 Ligands: GCS-KDO-KDO-GMH.2, FTT.13, FTT.15, PO4.17 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.263, B:L.267, B:F.288, B:F.288, A:V.71 Hydrogen bonds: A:R.78

1 x DPO: DIPHOSPHATE(Non-functional Binders)

DPO.18: 3 residues within 4Å: Ligands: GMH-GLC-GLC-GLC-GMH.1, GMH-GLC-GLC-GLC-GMH.1, GCS-KDO-KDO-GMH.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ho, H. et al., Structural basis for dual-mode inhibition of the ABC transporter MsbA. Nature (2018)

Release Date

2018-05-02

Peptides

Lipid A export ATP-binding/permease protein MsbA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Lipid A export ATP-binding/permease protein MsbA

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