SMTL ID : 4isa.1

Crystal Structure of the Escherichia coli LpxC/BB-78485 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.79, H.238, D.242 Ligands: GVR.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.79, A:H.238, A:D.242, A:D.242

2 x GVR: (2R)-N-hydroxy-3-naphthalen-2-yl-2-[(naphthalen-2-ylsulfonyl)amino]propanamide

GVR.2: 22 residues within 4Å: Chain A: L.18, M.61, L.62, C.63, T.76, E.78, H.79, I.103, T.191, F.192, G.193, I.198, C.207, G.210, C.214, A.215, H.238, D.242, H.265 Ligands: ZN.1, FMT.9, FMT.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.18, A:L.18, A:T.191, A:I.198, A:I.198, A:A.215 Hydrogen bonds: A:E.78, A:E.78, A:E.78 GVR.3: 6 residues within 4Å: Chain A: L.116, D.180, M.183, R.184, P.300 Ligands: D1D.21 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.116 Hydrogen bonds: A:R.184

17 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 2 residues within 4Å: Chain A: R.204, L.206 Ligand excluded by PLIP FMT.5: 4 residues within 4Å: Chain A: M.195, I.198, E.199, S.211 Ligand excluded by PLIP FMT.6: 3 residues within 4Å: Chain A: A.181, R.184, Q.185 Ligand excluded by PLIP FMT.7: 1 residues within 4Å: Chain A: D.227 Ligand excluded by PLIP FMT.8: 3 residues within 4Å: Chain A: D.160, F.161, N.162 Ligand excluded by PLIP FMT.9: 6 residues within 4Å: Chain A: D.59, T.60, L.62, C.63, H.265 Ligands: GVR.2 Ligand excluded by PLIP FMT.10: 3 residues within 4Å: Chain A: M.104, D.105, P.110 Ligand excluded by PLIP FMT.11: 1 residues within 4Å: Chain A: R.131 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain A: F.161, F.192 Ligands: GVR.2 Ligand excluded by PLIP FMT.13: 1 residues within 4Å: Chain A: K.55 Ligand excluded by PLIP FMT.14: 1 residues within 4Å: Chain A: Y.113 Ligand excluded by PLIP FMT.15: 2 residues within 4Å: Chain A: W.144, Y.261 Ligand excluded by PLIP FMT.16: 2 residues within 4Å: Chain A: E.134, T.135 Ligand excluded by PLIP FMT.17: 6 residues within 4Å: Chain A: S.154, L.155, D.156, A.174, M.175, N.176 Ligand excluded by PLIP FMT.18: 1 residues within 4Å: Chain A: R.29 Ligand excluded by PLIP FMT.19: 2 residues within 4Å: Chain A: Y.284, T.286 Ligand excluded by PLIP FMT.20: 4 residues within 4Å: Chain A: F.153, N.253, I.254, F.297 Ligand excluded by PLIP

1 x D1D: (4S,5S)-1,2-DITHIANE-4,5-DIOL(Non-covalent)

D1D.21: 5 residues within 4Å: Chain A: Y.113, M.183, S.187, R.188 Ligands: GVR.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.188 Water bridges: A:R.188, A:R.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, C.J. et al., Structural Basis of the Promiscuous Inhibitor Susceptibility of Escherichia coli LpxC. Acs Chem.Biol. (2014)

Release Date

2013-10-30

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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