SMTL ID : 5u86.1

Structure of the Aquifex aeolicus LpxC/LPC-069 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.74, H.226, D.230 Ligands: 81V.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.74, A:H.226, A:D.230, A:D.230

1 x 81V: N-[(2S,3S)-4,4-difluoro-3-hydroxy-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]-4-({4-[(morpholin-4-yl)methyl]phenyl}ethynyl)benzamide(Non-covalent)

81V.2: 21 residues within 4Å: Chain A: I.18, H.19, H.58, E.73, H.74, T.179, F.180, A.181, I.186, G.198, S.199, L.200, T.203, V.205, Y.212, H.226, K.227, D.230, H.253 Ligands: ZN.1, PO4.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.18, A:F.180, A:A.181, A:I.186, A:T.203, A:V.205 Hydrogen bonds: A:H.58, A:H.58, A:E.73, A:T.179 Water bridges: A:T.179, A:T.179, A:K.227

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: E.127, E.128, L.263, Q.267 Ligand excluded by PLIP

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 7 residues within 4Å: Chain A: T.56, N.57, H.58, K.227, G.252, H.253 Ligands: 81V.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.58, A:H.58, A:H.253 Water bridges: A:K.227, A:K.227, A:K.227, A:K.227, A:S.254 Salt bridges: A:H.58, A:K.227, A:H.253 PO4.5: 3 residues within 4Å: Chain A: N.57, H.58, H.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.57 Water bridges: A:N.57 Salt bridges: A:H.58, A:H.188

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

EDO.6: 4 residues within 4Å: Chain A: D.122, Y.123, F.124, S.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.122 Water bridges: A:V.125 EDO.7: 3 residues within 4Å: Chain A: F.40, Y.45, T.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.31 EDO.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lemaitre, N. et al., Curative Treatment of Severe Gram-Negative Bacterial Infections by a New Class of Antibiotics Targeting LpxC. MBio (2017)

Release Date

2017-08-09

Peptides

UDP-3-O-acyl-N-acetylglucosamine deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-3-O-acyl-N-acetylglucosamine deacetylase