SMTL ID : 7ap2.1

Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound LeuS7HMDDA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: W.224, L.430, R.431, D.432, W.433, Y.555 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.224, A:Y.555 Water bridges: A:D.432, A:G.434 EDO.2: 4 residues within 4Å: Chain A: W.224, Y.340, R.429, L.430 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.224, A:Y.340, A:Y.340 Water bridges: A:R.431

1 x RRW: [(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate(Non-covalent)

RRW.3: 23 residues within 4Å: Chain A: M.41, F.42, P.43, Y.44, H.50, G.52, H.53, N.56, Y.57, D.81, S.511, Y.514, Y.542, G.544, G.545, E.547, H.548, H.552, Q.581, G.582, M.583, V.584, K.635 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:M.41, A:F.42 Hydrogen bonds: A:F.42, A:Y.44, A:D.81, A:G.545, A:E.547, A:G.582, A:V.584, A:V.584 Water bridges: A:E.547 Salt bridges: A:H.53 pi-Stacking: A:H.53

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.450, C.453, C.491, C.494 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.450, A:C.453, A:C.491, A:C.494

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, B. et al., Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors. Molecules (2020)

Release Date

2020-10-28

Peptides

Leucine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Leucine--tRNA ligase

Related Entries With Identical Sequence