SMTL ID : 8i1y.1

The structure of E. coli TrpRS bound with a chemical fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

1 x O7L: 5-ethanoylthiophene-2-carbonitrile(Non-covalent)

O7L.1: 13 residues within 4Å: Chain A: A.89, G.92, W.93, N.96, D.127, L.131 Chain B: A.89, G.92, W.93, N.96, D.127, V.130, L.131 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.93, A:L.131 Hydrogen bonds: A:N.96

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

SO4.2: 3 residues within 4Å: Chain A: M.269, Y.270, G.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.270, A:G.271 Water bridges: A:H.272 SO4.3: 4 residues within 4Å: Chain A: N.20, S.197, K.198, S.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.20, A:K.198 SO4.4: 4 residues within 4Å: Chain A: Y.100, G.102, E.103, R.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.102, A:E.103 Water bridges: A:F.101 Salt bridges: A:R.106 SO4.6: 5 residues within 4Å: Chain B: K.113, K.195, S.197, K.198, S.199 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.198, B:S.199 Water bridges: B:K.113, B:R.116, B:K.195, B:K.195, B:K.195, B:K.195, B:K.195, B:S.197, B:K.198, B:K.198, B:S.199, B:S.199 Salt bridges: B:K.113, B:K.195, B:K.198 SO4.7: 5 residues within 4Å: Chain B: K.58, D.62, Y.292, H.293, R.296 4 PLIP interactions: 4 interactions with chain B Water bridges: B:H.293, B:N.297 Salt bridges: B:K.58, B:H.293

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

TYM.5: 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: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:Q.11, B:P.145, B:E.148, B:D.149, B:Q.150 Salt bridges: B:K.198

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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