- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.84 Å
- Oligo State
- homo-dimer
- Ligands
- 9 x GOL: GLYCEROL(Non-functional Binders)
- 6 x NA: SODIUM ION(Non-functional Binders)
NA.5: 3 residues within 4Å:- Chain A: E.384, S.387
- Ligands: FZK.7
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.384, A:S.387
- Water bridges: A:K.369
NA.6: 3 residues within 4Å:- Chain A: N.170, S.379
- Ligands: MLI.8
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.170, A:S.379
NA.14: 4 residues within 4Å:- Chain B: K.369, E.384, S.387
- Ligands: FZK.18
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:K.369, B:S.387, B:S.387
NA.15: 3 residues within 4Å:- Chain B: L.407, T.410, Q.413
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:T.410
NA.16: 2 residues within 4Å:- Chain B: N.162, T.164
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:T.164
- Water bridges: B:N.162, B:T.163
NA.17: 3 residues within 4Å:- Chain B: N.170, S.379
- Ligands: MLI.19
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:N.170, B:S.379
- 2 x FZK: 5'-O-(N-(L-seryl)-Sulfamoyl)uridine(Non-covalent)
FZK.7: 19 residues within 4Å:- Chain A: T.264, E.266, R.295, F.309, R.310, V.311, F.314, K.316, E.318, E.384, L.385, V.386, S.387, N.423, G.424, T.425, A.428, R.431
- Ligands: NA.5
17 PLIP interactions:17 interactions with chain A- Hydrogen bonds: A:E.266, A:R.295, A:F.309, A:V.311, A:K.316, A:E.318, A:E.384, A:S.387, A:T.425, A:R.431, A:R.431, A:R.431
- Water bridges: A:S.387, A:R.431
- Salt bridges: A:R.295
- pi-Stacking: A:F.314
- pi-Cation interactions: A:R.431
FZK.18: 20 residues within 4Å:- Chain B: T.264, E.266, R.295, E.297, F.309, R.310, V.311, F.314, K.316, E.318, E.384, L.385, V.386, S.387, N.423, G.424, T.425, A.428, R.431
- Ligands: NA.14
22 PLIP interactions:22 interactions with chain B- Hydrogen bonds: B:T.264, B:R.295, B:F.309, B:V.311, B:K.316, B:E.318, B:E.384, B:E.384, B:S.387, B:T.425, B:T.425, B:R.431, B:R.431, B:R.431
- Water bridges: B:R.295, B:R.295, B:S.387, B:T.430, B:R.431
- Salt bridges: B:R.295
- pi-Stacking: B:F.314
- pi-Cation interactions: B:R.431
- 3 x MLI: MALONATE ION(Non-functional Binders)
MLI.8: 7 residues within 4Å:- Chain A: N.170, H.171, V.172, L.306, F.309, R.383
- Ligands: NA.6
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:V.172
- Hydrogen bonds: A:N.170
- Salt bridges: A:H.171, A:R.383
MLI.19: 6 residues within 4Å:- Chain B: N.170, H.171, V.172, L.306, R.383
- Ligands: NA.17
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:V.172
- Hydrogen bonds: B:N.170, B:L.306, B:L.306
- Salt bridges: B:H.171, B:R.383
MLI.20: 6 residues within 4Å:- Chain B: W.277, R.402, N.406, L.407, R.408, K.416
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:N.406, B:L.407, B:R.408
- Water bridges: B:K.416, B:K.416
- Salt bridges: B:R.402, B:K.416
- 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
- 2020-01-08
- Peptides
- Seryl-tRNA synthetase, putative: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.84 Å
- Oligo State
- homo-dimer
- Ligands
- 9 x GOL: GLYCEROL(Non-functional Binders)
- 6 x NA: SODIUM ION(Non-functional Binders)
- 2 x FZK: 5'-O-(N-(L-seryl)-Sulfamoyl)uridine(Non-covalent)
- 3 x MLI: MALONATE ION(Non-functional Binders)
- 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
- 2020-01-08
- Peptides
- Seryl-tRNA synthetase, putative: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B