SMTL ID : 7ap3.1

Crystal structure of E. coli tyrosyl-tRNA synthetase in complex with TyrS7HMDDA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x RRB: [(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate(Non-covalent)

RRB.1: 26 residues within 4Å: Chain A: Y.37, G.39, F.40, D.41, H.48, 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, V.225, P.226, L.227, I.228 Ligands: NA.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.37, A:V.53, A:L.71, A:Q.179, A:L.227 Hydrogen bonds: A:Y.37, A:Y.37, A:D.41, A:D.81, A:Q.179, A:D.182, A:G.198, A:D.200, A:Q.201, A:N.204, A:P.226, A:I.228, A:I.228 Salt bridges: A:H.51 RRB.3: 26 residues within 4Å: Chain B: Y.37, G.39, F.40, D.41, H.48, 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, V.225, P.226, L.227, I.228, F.236 Ligands: NA.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.37, B:L.71, B:Q.179, B:L.227 Hydrogen bonds: B:Y.37, B:D.41, B:D.41, B:Y.175, B:Q.179, B:G.198, B:Q.201, B:N.204, B:I.228, B:I.228 Water bridges: B:D.81, B:K.85, B:K.85, B:D.200, B:D.200

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: C.38, G.39, Q.201 Ligands: RRB.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.39 NA.4: 4 residues within 4Å: Chain B: C.38, G.39, Q.201 Ligands: RRB.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.39, B:G.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, B. et al., Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors. Molecules (2020)

Release Date

2020-10-28

Peptides

Tyrosine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tyrosine--tRNA ligase

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