SMTL ID : 6pj3.1

Crystal structure of the Klebsiella pneumoniae LpxH/JH-LPH-33 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, A:H.10, A:D.41, A:H.197, H2O.2 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.2

1 x OKY: 1-[5-({4-[3-chloro-5-(trifluoromethyl)phenyl]piperazin-1-yl}sulfonyl)-2,3-dihydro-1H-indol-1-yl]ethan-1-one(Non-covalent)

OKY.3: 17 residues within 4Å: Chain A: A.45, W.46, N.79, R.80, F.82, L.83, Y.125, F.128, V.132, I.137, Q.138, F.141, I.152, A.153, M.156, R.157, S.160 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.82, A:Y.125, A:I.137, A:F.141 Hydrogen bonds: A:W.46, A:R.157 Water bridges: A:N.79 pi-Stacking: A:F.141 pi-Cation interactions: A:R.80

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: D.51, N.53, H.56, H.150, R.157 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.53, A:H.56, A:R.157, A:R.157 Water bridges: A:H.150 EDO.5: 3 residues within 4Å: Chain A: Y.37, Y.74, L.103 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cho, J. et al., Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-02-12

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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