SMTL ID : 7cms.1

Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with chuangxinmycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: 11 residues within 4Å: Chain A: F.5, G.7, V.40, H.43, Y.125, M.129, D.132, I.133, V.141, V.143, Q.147 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.5, A:F.5, A:I.133, A:V.141, A:V.143 Hydrogen bonds: A:D.132, A:D.132 Water bridges: A:G.7 9E0.3: 11 residues within 4Å: Chain B: F.5, G.7, V.40, H.43, M.129, D.132, I.133, V.141, V.143, Q.147, K.195 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.5, B:F.5, B:I.133, B:V.141, B:V.143 Hydrogen bonds: B:D.132 Water bridges: B:Q.147 Salt bridges: B:K.195

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: K.192, S.194, K.195 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.195 Water bridges: A:K.192, A:M.193 Salt bridges: A:K.192, A:K.195 PO4.4: 3 residues within 4Å: Chain B: K.192, S.194, K.195 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.195 Water bridges: B:T.15, B:N.18, B:N.18, B:N.18, B:N.18, B:S.194 Salt bridges: B:K.192, B:K.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, S. et al., Structural insights into the specific interaction between Geobacillus stearothermophilus tryptophanyl-tRNA synthetase and antimicrobial Chuangxinmycin. J.Biol.Chem. (2022)

Release Date

2021-08-04

Peptides

Tryptophan--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan--tRNA ligase

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