SMTL ID : 8c9g.1 (1 other biounit)

Priestia megaterium mupirocin-sensitive isoleucyl-tRNA synthetase 1 complexed with mupirocin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 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 ZN.6: 4 residues within 4Å: Chain B: C.887, C.890, C.907, C.910 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.887, B:C.890, B:C.907, B:C.910

2 x MRC: MUPIROCIN(Non-covalent)

MRC.2: 22 residues within 4Å: Chain A: P.56, P.57, Y.58, H.64, G.66, H.67, N.70, W.527, S.530, E.553, G.554, D.556, Q.557, W.561, H.584, G.585, F.586, A.587, M.595, S.596, K.597, V.602 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.527, A:Q.557, A:W.561, A:F.586, A:F.586, A:F.586, A:V.602, A:V.602 Hydrogen bonds: A:Y.58, A:G.554, A:D.556, A:Q.557, A:A.587, A:M.595, A:K.597 Water bridges: A:S.530 Salt bridges: A:H.64 MRC.7: 20 residues within 4Å: Chain B: P.56, P.57, Y.58, H.64, G.66, H.67, N.70, S.530, E.553, G.554, D.556, Q.557, W.561, H.584, G.585, F.586, A.587, M.595, S.596, K.597 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:E.553, B:W.561, B:F.586, B:F.586, B:F.586, B:M.595 Hydrogen bonds: B:Y.58, B:E.553, B:G.554, B:D.556, B:Q.557, B:A.587, B:K.597 Salt bridges: B:H.64

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

CL.3: 1 residues within 4Å: Chain A: K.430 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.447, W.450, N.563 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: K.686 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

NA.5: 1 residues within 4Å: Chain A: E.331 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.331 NA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.13: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.84

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain B: K.430, D.696, Y.698 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.430 GOL.9: 3 residues within 4Å: Chain B: E.138, Q.139, R.142 No protein-ligand interaction detected (PLIP)

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

2023-08-23

Peptides

Isoleucine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoleucine--tRNA ligase

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