SMTL ID : 3p3g.1

Crystal Structure of the Escherichia coli LpxC/LPC-009 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: E.78, H.79, T.191, H.238, D.242 Ligands: 3P3.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.79, A:H.238, A:D.242, A:D.242

1 x 3P3: N-[(1S,2R)-2-hydroxy-1-(hydroxycarbamoyl)propyl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide(Non-covalent)

3P3.2: 23 residues within 4Å: Chain A: L.18, M.61, L.62, C.63, E.78, H.79, T.191, F.192, M.195, I.198, Q.202, C.207, G.210, S.211, F.212, A.215, V.217, H.238, K.239, D.242, H.265 Ligands: ZN.1, SO4.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.62, A:T.191, A:F.192, A:I.198, A:A.215 Hydrogen bonds: A:C.63, A:E.78, A:T.191, A:T.191, A:K.239, A:H.265, A:H.265 pi-Stacking: A:F.212

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: K.22, K.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.23 Water bridges: A:K.22, A:K.23 Salt bridges: A:K.22 SO4.4: 1 residues within 4Å: Chain A: K.22 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.22 SO4.5: 3 residues within 4Å: Chain A: R.29, R.40, V.93 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.95, A:E.95 Water bridges: A:R.29, A:R.40, A:R.40 Salt bridges: A:R.40 SO4.6: 4 residues within 4Å: Chain A: K.8, R.9, G.119, I.120 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.119, A:I.120, A:I.120 Salt bridges: A:R.9 SO4.7: 6 residues within 4Å: Chain A: D.59, K.239, G.264, H.265, A.266 Ligands: 3P3.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.265 Water bridges: A:C.63 Salt bridges: A:K.239, A:H.265

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 8 residues within 4Å: Chain A: F.161, H.163, I.166, F.192, G.193, F.194, V.218, F.235 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.194

1 x UKW: 4-ethynyl-N-[(1S,2R)-2-hydroxy-1-(oxocarbamoyl)propyl]benzamide(Non-covalent)

UKW.9: 5 residues within 4Å: Chain A: M.61, F.194, D.197, Y.200, L.201 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.200, A:L.201 Hydrogen bonds: A:D.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, C.J. et al., Species-specific and inhibitor-dependent conformations of LpxC: implications for antibiotic design. Chem.Biol. (2011)

Release Date

2011-01-05

Peptides

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

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