SMTL ID : 8c9d.1

Priestia megaterium W130Q mutant of type 2 isoleucyl-tRNA synthetase complexed with an isoleucyl-adenylate analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.181, C.184, C.387, C.390 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.181, A:C.184, A:C.387, A:C.390 ZN.2: 4 residues within 4Å: Chain A: C.459, C.462, C.500, C.503 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.459, A:C.462, A:C.500, A:C.503

1 x ILA: N-[ISOLEUCINYL]-N'-[ADENOSYL]-DIAMINOSUFONE(Non-covalent)

ILA.3: 18 residues within 4Å: Chain A: G.45, P.46, P.47, T.48, H.54, G.56, H.57, D.85, W.517, S.520, E.549, G.550, D.552, Q.553, W.557, H.582, V.583, K.590 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.517, A:W.557 Hydrogen bonds: A:P.46, A:T.48, A:D.85, A:D.85, A:E.549, A:G.550, A:D.552, A:Q.553, A:V.583, A:V.583 Water bridges: A:T.48, A:L.59, A:R.61, A:K.64, A:Q.130, A:K.590 pi-Stacking: A:H.57, A:H.582, A:H.582

4 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.4: 3 residues within 4Å: Chain A: G.430, R.431, K.434 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.431 Water bridges: A:R.431 Salt bridges: A:R.431 TAR.5: 3 residues within 4Å: Chain A: Y.655, W.725, K.965 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.965 TAR.6: 4 residues within 4Å: Chain A: Q.98, S.122, V.125, Y.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.98, A:Q.98, A:Y.126 Water bridges: A:S.122, A:Y.126 TAR.7: 6 residues within 4Å: Chain A: A.622, W.624, G.697, F.698, T.699, S.700 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.696, A:T.699, A:S.700

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brkic, A. et al., Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif. Nat Commun (2023)

Release Date

2023-08-16

Peptides

Isoleucine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoleucine--tRNA ligase