SMTL ID : 6hdz.1

Pseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-Sulfamoyl)uridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: K.130, E.316, P.318, N.401, Y.402 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.402 Water bridges: A:T.128, A:K.130, A:R.410 EDO.2: 8 residues within 4Å: Chain A: M.165, H.173, M.277, Q.282, F.283, D.284, G.392 Chain B: Y.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.284, A:D.284, A:G.392 EDO.3: 6 residues within 4Å: Chain A: Q.209, P.232, T.233, E.235, R.264 Ligands: FZK.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.209, A:E.235 EDO.6: 5 residues within 4Å: Chain B: K.130, E.316, P.318, N.401, Y.402 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.402 Water bridges: B:T.128 EDO.7: 1 residues within 4Å: Chain B: E.122 No protein-ligand interaction detected (PLIP) EDO.8: 8 residues within 4Å: Chain A: Y.194 Chain B: M.165, H.173, M.277, Q.282, F.283, D.284, G.392 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.284, B:G.392

2 x FZK: 5'-O-(N-(L-seryl)-Sulfamoyl)uridine(Non-covalent)

FZK.4: 20 residues within 4Å: Chain A: T.233, E.235, R.264, I.278, R.279, Q.280, F.283, K.285, E.287, E.351, I.352, S.353, S.354, N.385, G.386, S.387, A.390, R.393 Ligands: EDO.3, NA.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:E.235, A:R.264, A:I.278, A:Q.280, A:K.285, A:E.351, A:E.351, A:S.354, A:S.387, A:R.393, A:R.393, A:R.393 Salt bridges: A:R.264 pi-Stacking: A:F.283 pi-Cation interactions: A:R.393 FZK.9: 19 residues within 4Å: Chain B: T.233, E.235, R.264, I.278, R.279, Q.280, F.283, K.285, E.287, E.351, I.352, S.353, S.354, N.385, G.386, S.387, A.390, R.393 Ligands: NA.10 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:E.235, B:R.264, B:I.278, B:Q.280, B:K.285, B:E.287, B:E.351, B:S.354, B:S.387, B:R.393, B:R.393, B:R.393 Water bridges: B:R.264, B:S.354 Salt bridges: B:R.264 pi-Stacking: B:F.283 pi-Cation interactions: B:R.393

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

NA.5: 3 residues within 4Å: Chain A: E.351, S.354 Ligands: FZK.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.351, A:S.354 NA.10: 3 residues within 4Å: Chain B: E.351, S.354 Ligands: FZK.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.354, B:S.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, L. et al., Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases. Acs Chem.Biol. (2020)

Release Date

2019-12-04

Peptides

Serine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine--tRNA ligase

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