SMTL ID : 6i5y.1

Crystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyrosyl)sulfamoyl-adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x YSA: 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE(Non-covalent)

YSA.1: 23 residues within 4Å: Chain A: Y.37, G.39, F.40, D.41, G.50, H.51, V.53, P.54, L.71, T.76, D.81, N.126, Y.175, Q.179, D.182, Q.195, G.197, G.198, D.200, Q.201, P.226, L.227, I.228 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.37, A:L.71, A:Q.179 Hydrogen bonds: A:Y.37, A:D.41, A:D.41, A:Y.175, A:Q.179, A:G.198, A:D.200, A:Q.201, A:N.204, A:I.228, A:I.228 Water bridges: A:G.39 Salt bridges: A:H.51 YSA.3: 23 residues within 4Å: Chain B: Y.37, G.39, F.40, D.41, G.50, H.51, V.53, P.54, L.71, T.76, D.81, N.126, Y.175, Q.179, D.182, Q.195, G.197, G.198, D.200, Q.201, P.226, L.227, I.228 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.37, B:L.71, B:Q.179 Hydrogen bonds: B:Y.37, B:D.41, B:D.81, B:Q.179, B:D.182, B:D.182, B:G.198, B:D.200, B:Q.201, B:I.228, B:I.228 Water bridges: B:G.39, B:D.81, B:K.85, B:K.85, B:K.85 Salt bridges: B:H.51

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

EDO.2: 4 residues within 4Å: Chain A: P.110, F.111, L.310, V.311 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.311 EDO.4: 4 residues within 4Å: Chain B: P.33, I.34, K.67, E.118 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.33, B:E.118 EDO.5: 6 residues within 4Å: Chain B: I.386, E.389, K.390, Q.391, Y.396, E.402 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.391 Water bridges: B:E.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nautiyal, M. et al., Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases. Eur.J.Med.Chem. (2019)

Release Date

2019-04-17

Peptides

Tyrosine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tyrosine--tRNA ligase

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