SMTL ID : 5tv4.1

3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.20 Å

Oligo State

homo-dimer

Ligands

1 x PA1- PA1- KDO- GMH- GMH- GMH- KDO: 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-alpha-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose

PA1-PA1-KDO-GMH-GMH-GMH-KDO.1: 12 residues within 4Å: Chain A: R.319, Q.330 Chain B: R.319 Ligands: PO4.2, PO4.3, PO4.4, PO4.5, FTT.6, FTT.8, DAO.9, FTT.10, FTT.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.319

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

PO4.2: 5 residues within 4Å: Chain A: R.101, R.319 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, FTT.10, FTT.11 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.101, A:R.319 PO4.3: 2 residues within 4Å: Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, PA1-PA1-KDO-GMH-GMH-GMH-KDO.1 No protein-ligand interaction detected (PLIP) PO4.4: 1 residues within 4Å: Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1 No protein-ligand interaction detected (PLIP) PO4.5: 4 residues within 4Å: Chain B: R.101 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, FTT.6, FTT.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.101, A:K.322 Hydrogen bonds: A:Q.279

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

FTT.6: 8 residues within 4Å: Chain B: D.64, L.68, R.101 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, PO4.5, MYR.7, FTT.8, DAO.9 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.64, B:L.68 FTT.8: 7 residues within 4Å: Chain B: I.315, A.316, R.319 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, PO4.5, FTT.6, DAO.9 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.316, B:R.319, B:R.319 Hydrogen bonds: B:R.319 FTT.10: 6 residues within 4Å: Chain A: R.319 Chain B: F.311, I.315 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, PO4.2, FTT.11 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.311, B:F.311, B:I.315 FTT.11: 6 residues within 4Å: Chain B: Q.279, S.283, L.286 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, PO4.2, FTT.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:S.283, B:L.286, B:L.286

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.7: 3 residues within 4Å: Chain B: L.68 Ligands: FTT.6, DAO.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.68

1 x DAO: LAURIC ACID(Non-covalent)

DAO.9: 7 residues within 4Å: Chain B: I.315, A.316 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, FTT.6, MYR.7, FTT.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.315, B:A.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mi, W. et al., Structural basis of MsbA-mediated lipopolysaccharide transport. Nature (2017)

Release Date

2017-09-20

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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