SMTL ID : 9m1f.1

Crystal structure of E. coli tryptophanyl-tRNA synthetase complexed with chuangxinmycin and ATP in closed-closed state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

2 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: 16 residues within 4Å: Chain A: F.7, S.8, G.9, A.10, Q.11, V.42, H.45, Y.128, M.132, D.135, I.136, V.144, V.146, Q.150 Ligands: ATP.2, MG.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.7, A:Q.11, A:V.42, A:I.136, A:V.144, A:V.146 Hydrogen bonds: A:Y.128, A:D.135 Water bridges: A:Q.109, A:Q.109, A:Q.150, A:Q.150 pi-Stacking: A:H.45 9E0.4: 17 residues within 4Å: Chain B: F.7, S.8, G.9, A.10, Q.11, V.42, H.45, Q.109, Y.128, M.132, D.135, I.136, V.144, V.146, Q.150 Ligands: ATP.5, MG.7 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.7, B:Q.11, B:V.42, B:I.136, B:V.144, B:V.146 Hydrogen bonds: B:Q.11, B:Y.128, B:Y.128, B:D.135, B:D.135 Water bridges: B:Q.150, B:Q.150, B:Q.150, B:Q.150

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 24 residues within 4Å: Chain A: G.9, A.10, Q.11, S.13, G.19, N.20, G.23, A.24, K.113, V.146, G.147, D.149, Q.150, G.183, A.184, R.185, V.186, K.195, M.196, S.197, K.198, S.199 Ligands: 9E0.1, MG.3 35 PLIP interactions: 35 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.11, A:S.13, A:N.20, A:G.23, A:G.147, A:D.149, A:V.186, A:K.195, A:M.196, A:M.196, A:K.198, A:S.199, A:S.199 Water bridges: A:S.13, A:N.20, A:W.28, A:K.113, A:K.113, A:K.113, A:K.113, A:K.113, A:P.145, A:E.148, A:E.148, A:S.199, A:S.199, A:S.199, A:S.199 Salt bridges: A:K.113, A:K.195, A:K.195, A:K.198, A:K.198, A:K.198 ATP.5: 24 residues within 4Å: Chain B: G.9, A.10, Q.11, S.13, G.19, N.20, G.23, A.24, K.113, V.146, G.147, D.149, Q.150, G.183, A.184, R.185, V.186, K.195, M.196, S.197, K.198, S.199 Ligands: 9E0.4, MG.7 33 PLIP interactions: 33 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:S.13, B:N.20, B:G.23, B:G.147, B:D.149, B:V.186, B:K.195, B:M.196, B:M.196, B:K.198, B:S.199, B:S.199 Water bridges: B:N.20, B:W.28, B:K.113, B:K.113, B:K.113, B:K.113, B:K.113, B:R.116, B:R.116, B:P.145, B:E.148, B:D.149, B:S.199 Salt bridges: B:K.113, B:K.195, B:K.195, B:K.198, B:K.198, B:K.198

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: Q.11 Ligands: 9E0.1, ATP.2 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: Q.11 Ligands: 9E0.4, ATP.5 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain B: Y.100, R.163 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.100, B:R.163 Water bridges: B:R.163

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

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