SMTL ID : 7ap4.1

Thermus thermophilus Aspartyl-tRNA Synthetase in Complex with Compound AspS7HMDDA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x RSN: (3~{S})-3-azanyl-4-[[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxysulfonylamino]-4-oxidanylidene-butanoic acid(Non-covalent)

RSN.1: 24 residues within 4Å: Chain A: S.200, Q.202, K.205, R.224, D.231, R.232, Q.233, F.236, Q.238, D.240, E.477, V.478, G.479, G.480, G.481, R.484, G.525, I.526, A.527, W.528, G.529, D.531, R.532, I.543 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.236, A:A.527 Hydrogen bonds: A:S.200, A:S.200, A:R.224, A:Q.233, A:Q.233, A:Q.238, A:E.477, A:E.477, A:G.529 Salt bridges: A:K.205, A:R.224, A:R.484 pi-Stacking: A:F.236, A:F.236 RSN.2: 28 residues within 4Å: Chain B: E.178, S.200, Q.202, K.205, R.224, E.226, R.229, D.231, R.232, Q.233, F.236, Q.238, D.240, H.444, E.477, V.478, G.479, G.480, G.481, R.484, G.525, I.526, A.527, W.528, G.529, D.531, R.532, I.543 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:A.527 Hydrogen bonds: B:E.178, B:R.224, B:Q.233, B:Q.233, B:Q.238, B:E.477, B:E.477, B:G.529, B:R.532, B:R.532 Water bridges: B:R.224, B:G.480, B:R.532 Salt bridges: B:K.205, B:R.224, B:H.444, B:R.484 pi-Stacking: B:F.236, B:F.236

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

2020-12-09

Peptides

Aspartate--tRNA(Asp) ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartate--tRNA(Asp) ligase

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