SMTL ID : 8wo3.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: W.236, T.237, T.238 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.238, A:T.238 Water bridges: A:W.236, A:T.238, A:H.325, A:H.397 GOL.3: 4 residues within 4Å: Chain A: T.14, S.17, M.18, K.669 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.14, A:S.17, A:M.18, A:K.669 GOL.4: 10 residues within 4Å: Chain A: A.198, E.199, A.200, R.464, W.467, R.576, G.577, Q.580, S.581, L.584 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.200, A:R.464, A:G.577, A:S.581 Water bridges: A:E.199

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

ACT.5: 6 residues within 4Å: Chain A: D.642, Y.643, Q.644, H.714, D.715, V.717 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.642, A:Y.643, A:Q.644, A:D.715 Water bridges: A:F.716

1 x MRC: MUPIROCIN(Non-covalent)

MRC.6: 25 residues within 4Å: Chain A: G.57, P.58, P.59, Y.60, H.66, L.67, G.68, H.69, N.72, D.97, W.542, S.545, E.570, G.571, D.573, Q.574, W.578, H.601, G.602, F.603, I.604, M.612, S.613, K.614, V.619 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.67, A:E.570, A:W.578, A:F.603, A:M.612, A:V.619 Hydrogen bonds: A:G.571, A:D.573, A:Q.574, A:I.604, A:K.614 Water bridges: A:Y.60 Salt bridges: A:H.66

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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