SMTL ID : 8i2a.1

E. coli tryptophanyl-tRNA synthetase bound with a chemical fragment at the dimerization interface

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: N.20, M.196, S.197, K.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.20, A:M.196, A:K.198 SO4.4: 5 residues within 4Å: Chain B: K.58, D.62, Y.292, H.293, R.296 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.297 Salt bridges: B:K.58, B:H.293

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

TYM.2: 28 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 Ligands: EDO.3 21 PLIP interactions: 21 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:P.145, B:E.148 Salt bridges: B:K.198

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

EDO.3: 5 residues within 4Å: Chain B: N.20, K.195, S.197, K.198 Ligands: TYM.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.20, B:K.195

1 x 5OB: 5-METHOXYBENZIMIDAZOLE(Non-covalent)

5OB.5: 13 residues within 4Å: Chain A: A.89, G.92, W.93, N.96, D.127, V.130, L.131 Chain B: A.89, G.92, W.93, N.96, D.127, L.131 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.93, A:W.93 Hydrogen bonds: B:D.127 pi-Stacking: A:W.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, M. et al., An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening. Nucleic Acids Res. (2023)

Release Date

2023-04-12

Peptides

Tryptophan--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan--tRNA ligase

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