SMTL ID : 8qjz.1

Crystal structure of E. coli LpxH in complex with lipid X

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.8, H.10, D.41, H.197 Ligands: MN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.8, A:D.41, A:H.197, H2O.3, H2O.3 MN.2: 6 residues within 4Å: Chain A: D.8, D.41, N.79, H.114, H.195 Ligands: MN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.41, A:H.114, A:H.195, H2O.3

1 x LP5: (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE(Non-covalent)

LP5.3: 20 residues within 4Å: Chain A: W.46, N.79, R.80, F.82, L.83, D.122, G.124, Y.125, F.128, L.137, F.141, A.153, M.156, R.157, N.159, S.160, A.163, N.164, K.167, H.195 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:F.82, A:F.128, A:F.128, A:L.137, A:F.141, A:F.141, A:F.141, A:A.153, A:N.159 Hydrogen bonds: A:N.79, A:R.157, A:S.160, A:S.160, A:S.160, A:N.164, A:K.167, A:K.167, A:K.167 Water bridges: A:R.80, A:R.80, A:R.80, A:D.122, A:R.157, A:R.157, A:H.195 Salt bridges: A:R.80, A:R.157, A:K.167, A:H.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huseby, D.L. et al., Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-04-17

Peptides

UDP-2,3-diacylglucosamine hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-2,3-diacylglucosamine hydrolase

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