SMTL ID : 6hb6.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

2 x YSU: [(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate(Non-covalent)

YSU.1: 20 residues within 4Å: Chain A: Y.37, G.39, F.40, D.41, G.50, H.51, 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, L.227 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.37, A:L.71, A:Q.179 Hydrogen bonds: A:Y.37, A:G.39, A:D.41, A:D.41, A:D.41, A:Y.175, A:Q.179, A:G.198, A:D.200, A:Q.201, A:N.204 Water bridges: A:G.39, A:G.50, A:D.81, A:K.85, A:K.85, A:D.200, A:D.200 Salt bridges: A:H.51 YSU.5: 20 residues within 4Å: Chain B: Y.37, G.39, F.40, D.41, G.50, H.51, 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, L.227 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:Y.37, B:G.39, B:D.41, B:D.41, B:D.81, B:Q.179, B:D.182, B:G.198, B:D.200, B:Q.201, B:N.204 Water bridges: B:G.39, B:G.50, B:D.81, B:K.85 Salt bridges: B:H.51

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

EDO.2: 5 residues within 4Å: Chain A: P.33, I.34, A.35, K.67, E.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.33 EDO.3: 6 residues within 4Å: Chain A: I.386, E.389, K.390, Q.391, Y.396, E.402 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.391, A:E.402 Water bridges: A:Y.396 EDO.6: 4 residues within 4Å: Chain B: P.110, F.111, L.310, V.311 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.311

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: F.397, F.398, R.403 Ligand excluded by PLIP

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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