SMTL ID : 8c9f.1

Priestia megaterium inactive HIGH motif mutant of type1 isoleucyl-tRNA synthetase complexed with an isoleucyl-adenylate analogue.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.887, C.890, C.907, C.910 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.887, A:C.890, A:C.907, A:C.910

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

ILA.2: 17 residues within 4Å: Chain A: G.55, P.56, P.57, Y.58, H.66, H.67, N.70, W.527, E.553, G.554, D.556, Q.557, H.584, G.585, F.586, A.587 Ligands: NA.18 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.527, A:E.553 Hydrogen bonds: A:P.56, A:Y.58, A:E.553, A:G.554, A:D.556, A:Q.557, A:A.587 pi-Cation interactions: A:H.66 ILA.3: 8 residues within 4Å: Chain A: R.205, A.207, D.367, N.370, K.371, T.374, L.386, F.388 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.205, A:A.207, A:N.370, A:K.371, A:K.371 pi-Stacking: A:F.388

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: A.195, E.196, R.447, D.449, W.450 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.196 Salt bridges: A:R.447 SO4.5: 5 residues within 4Å: Chain A: G.590, E.591, S.633, N.635, I.636 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.633 SO4.6: 2 residues within 4Å: Chain A: D.349, S.350 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.350, A:S.350, A:R.406 SO4.7: 1 residues within 4Å: Chain A: W.435 No protein-ligand interaction detected (PLIP) SO4.9: 2 residues within 4Å: Chain A: S.596, K.597 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.596, A:K.597 Salt bridges: A:K.597 SO4.10: 2 residues within 4Å: Chain A: R.43, R.47 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.43, A:R.47 SO4.11: 3 residues within 4Å: Chain A: E.437, T.438, Y.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.437, A:T.438

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 4 residues within 4Å: Chain A: E.496, R.497, E.498, D.501 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: A.499, K.519 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: T.106, R.113 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: T.233 Ligand excluded by PLIP

2 x LI: LITHIUM ION(Non-covalent)

LI.15: 2 residues within 4Å: Chain A: S.387, F.388 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.387, A:F.388 LI.16: 1 residues within 4Å: Chain A: E.642 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.642

4 x NA: SODIUM ION(Non-functional Binders)

NA.17: 1 residues within 4Å: Chain A: E.520 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.520 NA.18: 2 residues within 4Å: Chain A: D.556 Ligands: ILA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.556 NA.19: 1 residues within 4Å: Chain A: T.521 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.521, A:T.521 NA.20: 1 residues within 4Å: Chain A: E.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.115, A:E.115

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