SMTL ID : 6bpp.1

E. coli MsbA in complex with LPS and inhibitor G092

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

homo-dimer

Ligands

1 x PA1- GCS- KDO- GMH- GMH- GLC- GLC- GLC- GMH- KDO: 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-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose

PA1-GCS-KDO-GMH-GMH-GLC-GLC-GLC-GMH-KDO.1: 10 residues within 4Å: Chain B: R.78, R.296, K.299 Ligands: FTT.3, FTT.5, PO4.11, FTT.12, FTT.13, MYR.14, PO4.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.296, B:R.296, B:R.78, B:R.296 Salt bridges: B:R.296

2 x E1M: (2E)-3-{6-[(1S)-1-(3-amino-2,6-dichlorophenyl)ethoxy]-4-cyclopropylquinolin-3-yl}prop-2-enoic acid(Non-covalent)

E1M.2: 16 residues within 4Å: Chain A: F.157, L.171, L.174, A.175, V.178, S.179, I.182, R.190, I.255, A.259, L.263, M.291, L.294, M.295, L.298, K.299 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.171, A:L.174, A:A.175, A:V.178, A:I.182, A:I.182, A:I.255, A:A.259, A:L.294, A:L.294, A:M.295 Hydrogen bonds: A:M.291 Salt bridges: A:R.190, A:K.299 Halogen bonds: A:A.259 E1M.10: 16 residues within 4Å: Chain B: F.157, L.171, A.175, V.178, I.182, D.252, I.255, A.259, A.262, L.263, M.291, L.294, M.295, L.298, K.299, T.302 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.171, B:L.171, B:A.175, B:V.178, B:I.182, B:I.182, B:I.255, B:L.294, B:L.294, B:M.295, B:L.298 Hydrogen bonds: B:M.291 Salt bridges: B:K.299 Halogen bonds: B:A.259

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

FTT.3: 10 residues within 4Å: Chain A: Q.256, F.288, M.295 Chain B: M.44, V.71, R.78 Ligands: PA1-GCS-KDO-GMH-GMH-GLC-GLC-GLC-GMH-KDO.1, DAO.4, PO4.11, FTT.12 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.71, A:F.288 FTT.5: 10 residues within 4Å: Chain A: M.44, L.45, L.47, L.48, R.78, R.296 Ligands: PA1-GCS-KDO-GMH-GMH-GLC-GLC-GLC-GMH-KDO.1, FTT.13, MYR.14, PO4.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.45, A:L.47, A:L.48 Hydrogen bonds: A:R.78, A:R.78 FTT.12: 7 residues within 4Å: Chain A: I.292 Chain B: M.44, L.51, R.296 Ligands: PA1-GCS-KDO-GMH-GMH-GLC-GLC-GLC-GMH-KDO.1, FTT.3, DAO.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.292, B:L.51 Hydrogen bonds: B:A.293 FTT.13: 8 residues within 4Å: Chain A: L.48 Chain B: S.289, R.296 Ligands: PA1-GCS-KDO-GMH-GMH-GLC-GLC-GLC-GMH-KDO.1, PA1-GCS-KDO-GMH-GMH-GLC-GLC-GLC-GMH-KDO.1, DAO.4, FTT.5, MYR.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.48

1 x DAO: LAURIC ACID(Non-covalent)

DAO.4: 11 residues within 4Å: Chain A: T.285, F.288, S.289, I.292 Chain B: L.48, S.289, I.292, A.293 Ligands: FTT.3, FTT.12, FTT.13 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.48, B:I.292, A:I.292

7 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.6: 1 residues within 4Å: Chain A: F.43 No protein-ligand interaction detected (PLIP) 3PE.7: 2 residues within 4Å: Chain A: I.177, I.258 No protein-ligand interaction detected (PLIP) 3PE.8: 1 residues within 4Å: Chain A: I.170 No protein-ligand interaction detected (PLIP) 3PE.9: 1 residues within 4Å: Chain A: Y.268 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.268 3PE.16: 1 residues within 4Å: Chain B: I.158 No protein-ligand interaction detected (PLIP) 3PE.17: 1 residues within 4Å: Chain B: I.80 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.80 3PE.18: 1 residues within 4Å: Chain B: C.88 No protein-ligand interaction detected (PLIP)

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

PO4.11: 3 residues within 4Å: Chain B: R.78 Ligands: PA1-GCS-KDO-GMH-GMH-GLC-GLC-GLC-GMH-KDO.1, FTT.3 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.78 PO4.15: 4 residues within 4Å: Chain A: R.78 Chain B: Q.256 Ligands: PA1-GCS-KDO-GMH-GMH-GLC-GLC-GLC-GMH-KDO.1, FTT.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.256, B:Q.256 Salt bridges: A:R.78

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.14: 14 residues within 4Å: Chain A: M.44, L.51, V.71, M.75, R.78 Chain B: Q.256, S.260, L.263, L.267, F.288, M.295 Ligands: PA1-GCS-KDO-GMH-GMH-GLC-GLC-GLC-GMH-KDO.1, FTT.5, FTT.13 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.51, A:V.71, B:L.263, B:L.267, B:F.288 Hydrogen bonds: B:Q.256

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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