SMTL ID : 9kxr.1

Crystal structure of E. coli tryptophanyl-tRNA synthetase complexed with chuangxinmycin and tryptophanyl-5'-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

1 x 9E0: (5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid(Non-covalent)

9E0.1: 11 residues within 4Å: Chain A: F.7, G.9, Q.11, V.42, H.45, Y.128, M.132, D.135, I.136, V.144, Q.150 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.7, A:F.7, A:Q.11, A:V.42, A:I.136, A:V.144 Hydrogen bonds: A:Y.128, A:D.135

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

SO4.2: 4 residues within 4Å: Chain A: N.20, M.196, S.197, K.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.20, A:K.198 SO4.4: 4 residues within 4Å: Chain B: K.195, S.197, K.198, S.199 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.198 Water bridges: B:K.195, B:K.195 Salt bridges: B:K.195

1 x TYM: TRYPTOPHANYL-5'AMP(Non-covalent)

TYM.3: 27 residues within 4Å: Chain B: F.7, S.8, G.9, A.10, Q.11, G.19, N.20, G.23, A.24, V.42, H.45, Y.128, M.132, D.135, I.136, V.144, V.146, G.147, D.149, Q.150, G.183, A.184, R.185, V.186, K.195, M.196, K.198 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:F.7, B:V.42, B:I.136, B:V.144, B:V.146 Hydrogen bonds: B:Q.11, B:N.20, B:G.23, B:Y.128, B:Y.128, B:D.135, B:D.135, B:G.147, B:D.149, B:V.186, B:V.186, B:K.195, B:M.196 Water bridges: B:T.17, B:P.145, B:E.148, B:E.148, B:Q.150, B:Q.150 Salt bridges: B:K.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, Y. et al., Mechanistic insights into the ATP-mediated and species-dependent inhibition of TrpRS by chuangxinmycin. Rsc Chem Biol (2025)

Release Date

2025-07-23

Peptides

Tryptophan--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan--tRNA ligase

Related Entries With Identical Sequence