SMTL ID : 6pib.1

Structure of the Klebsiella pneumoniae LpxH-AZ1 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.9, H.11, D.42, H.198 Ligands: MN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.9, A:H.11, A:D.42, A:H.198, H2O.1 MN.2: 6 residues within 4Å: Chain A: D.9, D.42, N.80, H.115, H.196 Ligands: MN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.42, A:H.115, A:H.196, H2O.1

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

OKV.3: 15 residues within 4Å: Chain A: A.46, W.47, N.80, R.81, F.83, L.84, Y.126, F.129, I.138, F.142, I.153, A.154, M.157, R.158, S.161 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.83, A:L.84, A:Y.126, A:F.129, A:F.129, A:I.138, A:F.142, A:R.158 Hydrogen bonds: A:W.47, A:R.158 pi-Stacking: A:F.142 pi-Cation interactions: A:R.81, A:R.81

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 4 residues within 4Å: Chain A: P.146, L.147, F.148, R.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.147, A:R.150 PG4.5: 8 residues within 4Å: Chain A: V.2, A.3, E.30, Q.33, M.226, K.228, E.235, I.237 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.2, A:V.2, A:K.228, A:E.235 Water bridges: A:A.3 PG4.6: 3 residues within 4Å: Chain A: I.149, R.152, I.153 No protein-ligand interaction detected (PLIP)

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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