SMTL ID : 6b8b.1

E. coli LptB in complex with ADP and a novobiocin derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.42, Q.84, E.162 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.42, H2O.1, H2O.1, H2O.2, H2O.2

1 x CZJ: (3s,5s,7s)-N-{7-[(3-O-carbamoyl-6-deoxy-5-methyl-4-O-methyl-beta-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-1-ben zopyran-3-yl}tricyclo[3.3.1.1~3,7~]decane-1-carboxamide(Non-covalent)

CZJ.2: 5 residues within 4Å: Chain A: F.89, R.90, R.91, L.92, A.100 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.89, A:L.92 Hydrogen bonds: A:R.91 Water bridges: A:R.91

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 12 residues within 4Å: Chain A: Y.12, R.15, V.17, P.36, N.37, G.38, A.39, G.40, K.41, T.42, T.43 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.15, A:R.15, A:G.38, A:A.39, A:G.40, A:K.41, A:T.42, A:T.43, A:T.43 Water bridges: A:Y.12, A:N.37, A:T.42, A:T.42, A:T.42, A:E.162, A:E.162 Salt bridges: A:K.41 pi-Stacking: A:Y.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

May, J.M. et al., The Antibiotic Novobiocin Binds and Activates the ATPase That Powers Lipopolysaccharide Transport. J. Am. Chem. Soc. (2017)

Release Date

2017-12-06

Peptides

Lipopolysaccharide export system ATP-binding protein LptB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lipopolysaccharide export system ATP-binding protein LptB

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