SMTL ID : 6ph9.1

Crystal Structure of the Klebsiella pneumoniae LpxH-lipid X complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

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 MN.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.4: 1 residues within 4Å: Chain A: K.228 No protein-ligand interaction detected (PLIP)

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)

LP5.5: 19 residues within 4Å: Chain A: W.47, N.80, R.81, F.83, L.84, D.123, G.125, Y.126, F.129, F.142, A.154, M.157, R.158, S.161, A.164, N.165, K.168, M.173, H.196 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:F.83, A:F.129, A:F.129, A:F.142, A:F.142, A:F.142, A:F.142, A:F.142, A:A.154 Hydrogen bonds: A:N.80, A:N.80, A:R.158, A:S.161, A:S.161, A:N.165, A:K.168, A:K.168, A:K.168 Water bridges: A:R.81, A:R.81, A:R.158, A:R.158, A:M.173 Salt bridges: A:R.81, A:R.158, A:K.168, A:H.196

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

PG4.6: 2 residues within 4Å: Chain A: K.132, M.157 No protein-ligand interaction detected (PLIP) PG4.7: 7 residues within 4Å: Chain A: E.100, T.118, R.130, A.179, D.182, A.183, R.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.118, A:R.186 Water bridges: A:R.130

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 2 residues within 4Å: Chain A: E.171, D.174 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.171, A:D.174, H2O.1, H2O.2, H2O.4

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

EDO.9: 3 residues within 4Å: Chain A: Y.38, Y.75, L.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.102

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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