SMTL ID : 8wni.1

Crystal structure of H. pylori isoleucyl-tRNA synthetase (HpIleRS) in complex with Val

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.896, C.899, C.911, R.913, C.914 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.896, A:C.899, A:C.911, A:C.914

1 x VAL: VALINE(Non-covalent)

VAL.2: 8 residues within 4Å: Chain A: P.58, P.59, Y.60, D.97, W.542, S.545, Q.574, W.578 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.542, A:W.578 Hydrogen bonds: A:P.58, A:Y.60, A:D.97, A:D.97, A:Q.574, V.2

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: W.236, T.237, T.238 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.238, A:T.238 Water bridges: A:W.236, A:H.397 GOL.4: 5 residues within 4Å: Chain A: W.637, N.641, L.647, R.648, F.653 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.637, A:R.648 Water bridges: A:D.646 GOL.5: 8 residues within 4Å: Chain A: G.68, H.69, N.72, E.570, G.571, D.573, Q.574, H.601 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.69, A:E.570, A:G.571, A:D.573, A:Q.574 Water bridges: A:K.76 GOL.6: 6 residues within 4Å: Chain A: E.137, K.140, F.152, E.153, P.155, K.157 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.140, A:K.157, A:K.157 Water bridges: A:K.140 GOL.7: 4 residues within 4Å: Chain A: K.816, K.817, E.819 Ligands: TRS.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.816, A:K.816 Water bridges: A:K.817

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

ACT.8: 6 residues within 4Å: Chain A: N.641, D.642, Y.643, Q.644, D.715, V.717 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.643, A:Q.644 Hydrogen bonds: A:N.641, A:D.715 Water bridges: A:F.716

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.9: 5 residues within 4Å: Chain A: E.819, N.820, F.821, L.863 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.819, A:N.820

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Structural basis for substrate and antibiotic recognition by Helicobacter pylori isoleucyl-tRNA synthetase. Febs Lett. (2024)

Release Date

2024-02-14

Peptides

Isoleucine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoleucine--tRNA ligase

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