SMTL ID : 6mli.1

Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) R77A mutant from Salmonella typhimurium complexed with histidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

1 x HIS: HISTIDINE(Non-covalent)

HIS.1: 11 residues within 4Å: Chain A: Y.14, F.52, S.69, S.70, L.71, S.72, L.117, S.120, T.121, Q.122, D.161 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.72, A:S.72, A:T.121 Water bridges: A:S.69, A:S.69, A:T.121 pi-Stacking: A:Y.14, A:F.52 Salt bridges: H.1

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

ACT.2: 3 residues within 4Å: Chain A: D.32, N.35, E.36 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.35 Hydrogen bonds: A:E.36 Water bridges: A:I.31, A:D.32 ACT.3: 5 residues within 4Å: Chain A: A.90, D.91, K.186, F.191, G.192 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.191 Hydrogen bonds: A:D.91 Water bridges: A:D.91, A:G.194 ACT.4: 1 residues within 4Å: Chain A: Q.78 No protein-ligand interaction detected (PLIP) ACT.5: 2 residues within 4Å: Chain A: D.85, D.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.85, A:D.211 ACT.6: 3 residues within 4Å: Chain A: H.113, D.136, V.138 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.113 ACT.7: 4 residues within 4Å: Chain A: L.106, D.128, N.129, K.133 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.133 Water bridges: A:L.106 Salt bridges: A:K.133

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: E.25, F.26, I.31, N.35, W.47 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.25, A:F.26, A:N.35, A:N.35 Water bridges: A:G.24, A:E.25

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

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