SMTL ID : 6mln.1

Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) S72A mutant from Salmonella typhimurium complexed with arginine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x ARG: ARGININE(Non-covalent)

ARG.1: 13 residues within 4Å: Chain A: D.11, Y.14, F.52, S.69, S.70, L.71, A.72, R.77, L.117, S.120, T.121, Q.122, D.161 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:Y.14, A:F.52 Hydrogen bonds: A:D.11, A:A.72, A:T.121, A:D.161 Water bridges: A:T.121, A:T.121 Salt bridges: A:D.11, A:R.77 pi-Cation interactions: A:Y.14

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 1 residues within 4Å: Chain A: D.65 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.200 ACT.3: 2 residues within 4Å: Chain A: D.202, T.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.204 Water bridges: A:D.202

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: E.25, F.26, I.31, N.35, W.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.26, A:N.35, A:N.35 GOL.5: 7 residues within 4Å: Chain A: A.89, A.90, D.91, V.163, N.234, V.235 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.91, A:D.91, A:V.235 Water bridges: A:E.162 GOL.6: 5 residues within 4Å: Chain A: I.56, R.77, G.119, S.120, T.121 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.77 Water bridges: A:R.77, A:G.119, A:A.124 GOL.7: 4 residues within 4Å: Chain A: V.163, S.166, F.233 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.166, A:S.166 GOL.8: 2 residues within 4Å: Chain A: D.144, S.148 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vergara, R. et al., The interplay of protein-ligand and water-mediated interactions shape affinity and selectivity in the LAO binding protein. Febs J. (2020)

Release Date

2019-08-07

Peptides

Lysine/arginine/ornithine-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

Lysine/arginine/ornithine-binding periplasmic protein