SMTL ID : 8crj.1

Crystal structure of LplA1 in complex with lipoyl-AMP (Listeria monocytogenes)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x LAQ: 5'-O-[(R)-({5-[(3R)-1,2-DITHIOLAN-3-YL]PENTANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE(Non-covalent)

LAQ.1: 23 residues within 4Å: Chain A: Y.40, I.47, R.73, G.78, A.79, V.80, Y.81, H.82, N.86, K.135, G.138, N.139, H.151, G.152, T.153, M.155, V.163, L.167, S.181, V.182, R.183, S.184, V.186 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.47, A:V.80, A:V.80 Hydrogen bonds: A:G.78, A:A.79, A:Y.81, A:Y.81, A:K.135, A:T.153, A:V.182, A:R.183, A:S.184 Salt bridges: A:K.135, A:K.135

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: I.210 No protein-ligand interaction detected (PLIP)

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

SO4.3: 4 residues within 4Å: Chain A: N.51, G.76, G.77, I.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.51, A:G.77 Water bridges: A:N.51 SO4.4: 2 residues within 4Å: Chain A: T.144, K.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.145 Water bridges: A:G.146 Salt bridges: A:K.145 SO4.5: 4 residues within 4Å: Chain A: K.319, I.325, T.326, K.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.327 Salt bridges: A:K.319 SO4.6: 3 residues within 4Å: Chain A: P.251, K.252, Q.273 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.252, A:Q.273 Salt bridges: A:K.252, A:K.274 SO4.7: 2 residues within 4Å: Chain A: R.17 Ligands: GOL.15 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.17 SO4.8: 2 residues within 4Å: Chain A: R.116, Y.209 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.116 SO4.9: 1 residues within 4Å: Chain A: R.269 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.269 SO4.10: 2 residues within 4Å: Chain A: K.259, R.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.260 Salt bridges: A:K.259 SO4.11: 3 residues within 4Å: Chain A: E.61, R.170, K.171 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.171 Water bridges: A:E.61, A:R.170, A:K.259, A:K.259 Salt bridges: A:R.170

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

EDO.12: 2 residues within 4Å: Chain A: G.1, H.3 No protein-ligand interaction detected (PLIP) EDO.13: 8 residues within 4Å: Chain A: I.26, L.30, N.31, L.32, E.34, I.92, T.93, K.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.31, A:L.32, A:E.34 EDO.14: 9 residues within 4Å: Chain A: V.55, I.58, D.59, T.60, P.169, R.170, D.172, I.174, R.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.60, A:T.60, A:R.170, A:D.172

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 9 residues within 4Å: Chain A: R.17, V.70, G.241, N.242, W.243, N.246, Y.247 Ligands: SO4.7, GOL.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.17, A:R.17, A:N.246 GOL.16: 5 residues within 4Å: Chain A: G.241, N.242, W.243, K.305 Ligands: GOL.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.242, A:W.243 Water bridges: A:K.305, A:K.305 GOL.17: 3 residues within 4Å: Chain A: R.50, R.239, K.249 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.50, A:R.239, A:K.249, A:K.249 GOL.18: 2 residues within 4Å: Chain A: K.124, G.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dienemann, J.N. et al., A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites. Angew.Chem.Int.Ed.Engl. (2023)

Release Date

2023-06-07

Peptides

lipoate--protein ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

lipoate--protein ligase

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