SMTL ID : 4ehy.1

Crystal structure of LpxK from Aquifex aeolicus in complex with ADP/Mg2+ at 2.2 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 23 residues within 4Å: Chain A: G.48, S.49, G.50, K.51, T.52, S.53, M.56, E.100, L.103, R.206, F.208, L.235, G.236, Q.240, F.241, V.244, T.278, P.279, K.280, L.294, F.296 Ligands: CL.2, MG.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:S.49, A:G.50, A:K.51, A:T.52, A:T.52, A:T.52, A:R.206, A:R.206, A:G.236, A:Q.240, A:Q.240, A:K.280 Water bridges: A:G.47, A:K.51, A:K.51, A:K.51, A:S.53, A:S.53, A:D.237 Salt bridges: A:K.51, A:K.280, A:K.280 pi-Stacking: A:F.241, A:F.296

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

CL.2: 5 residues within 4Å: Chain A: G.50, S.53, R.206, F.296 Ligands: ADP.1 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.100 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.100, H2O.1, H2O.1, H2O.1, H2O.1

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: G.88, N.89, L.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.90 GOL.5: 3 residues within 4Å: Chain A: E.189, F.208, N.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.247 GOL.6: 3 residues within 4Å: Chain A: E.271, G.272, N.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.272, A:N.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Emptage, R.P. et al., Crystal structure of LpxK, the 4'-kinase of lipid A biosynthesis and atypical P-loop kinase functioning at the membrane interface. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-08-29

Peptides

Tetraacyldisaccharide 4'-kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tetraacyldisaccharide 4'-kinase

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