SMTL ID : 4mdt.1 (3 other biounits)

Structure of LpxC bound to the reaction product UDP-(3-O-(R-3-hydroxymyristoyl))-glucosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.79, T.191, H.238, D.242 Ligands: PO4.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.79, A:H.238, A:D.242, A:D.242

1 x 24G: uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-glucosamine(Non-covalent)

24G.2: 21 residues within 4Å: Chain A: L.18, L.62, K.143, I.159, D.160, F.161, T.191, F.192, M.195, I.198, C.207, G.210, S.211, A.215, V.217, K.239, K.262, S.263, G.264, H.265 Ligands: PO4.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.18, A:L.18, A:I.198, A:I.198, A:I.198, A:A.215 Hydrogen bonds: A:T.60, A:L.62, A:K.143, A:K.143, A:D.160, A:D.160, A:T.191, A:F.192, A:K.239, A:H.265 Water bridges: A:D.197, A:D.197 Salt bridges: A:K.143, A:K.239, A:K.239, A:K.239, A:H.265

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

PO4.3: 9 residues within 4Å: Chain A: L.62, E.78, H.79, T.191, H.238, D.242, H.265 Ligands: ZN.1, 24G.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.242 Salt bridges: A:H.79, A:H.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clayton, G.M. et al., Structure of the Bacterial Deacetylase LpxC Bound to the Nucleotide Reaction Product Reveals Mechanisms of Oxyanion Stabilization and Proton Transfer. J.Biol.Chem. (2013)

Release Date

2013-10-16

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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