SMTL ID : 7d5c.1

IleRS in complex with a tRNA site inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x GVU: (2E,4S,5S,6E,8E)-10-[(2S,3R,6S,8R,9S)-3-butyl-9-methyl-2-[(1E,3E)-3-methyl-5-oxidanyl-5-oxidanylidene-penta-1,3-dienyl]-3-(4-oxidanyl-4-oxidanylidene-butanoyl)oxy-1,7-dioxaspiro[5.5]undecan-8-yl]-4,8-dimethyl-5-oxidanyl-deca-2,6,8-trienoic acid(Non-covalent)

GVU.1: 21 residues within 4Å: Chain A: F.48, G.88, V.89, P.90, F.191, W.402, R.454, W.456, R.460, R.462, D.527, C.528, W.529, D.564, Q.565, R.567, G.568, T.572, S.604, K.605, S.606 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:F.48, A:V.89, A:F.191, A:F.191, A:F.191, A:W.402, A:W.529, A:W.529, A:D.564, A:T.572 Hydrogen bonds: A:V.89, A:D.455, A:R.460, A:D.527, A:K.605, A:S.606 Water bridges: A:S.189, A:R.454, A:R.454, A:R.454, A:R.462, A:R.462, A:R.462, A:R.567 Salt bridges: A:R.454, A:R.462, A:K.605

1 x GV6: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S,3S)-2-azanyl-3-methyl-pentanoate(Non-covalent)

GV6.2: 18 residues within 4Å: Chain A: G.45, P.46, P.47, F.48, H.54, G.56, H.57, D.85, W.529, S.532, E.561, G.562, Q.565, W.569, G.593, I.594, V.595 Ligands: EDO.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.529, A:E.561 Hydrogen bonds: A:F.48, A:D.85, A:G.562, A:Q.565, A:V.595, A:V.595 Water bridges: A:H.57, A:H.57, A:K.64, A:K.605 Salt bridges: A:H.57

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: R.251, L.265, Y.266, L.389 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.251 EDO.4: 7 residues within 4Å: Chain A: S.430, K.433, S.434, P.555, S.583, V.584, Y.586 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.430, A:S.583 EDO.5: 5 residues within 4Å: Chain A: G.562, L.563, D.564, I.594 Ligands: GV6.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.564, A:D.564

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, B. et al., Inhibitory mechanism of reveromycin A at the tRNA binding site of a class I synthetase. Nat Commun (2021)

Release Date

2021-02-24

Peptides

Isoleucine--tRNA ligase, cytoplasmic: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoleucine--tRNA ligase, cytoplasmic