SMTL ID : 8tc9.1 (1 other biounit)

Human asparaginyl-tRNA synthetase bound to OSM-S-106

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x ZTE: N~1~-[(3M)-3-(4-aminothieno[3,2-d]pyrimidin-6-yl)benzene-1-sulfonyl]-L-aspartamide(Non-covalent)

ZTE.1: 23 residues within 4Å: Chain A: V.278, E.279, S.299, Q.301, R.322, E.324, R.330, H.331, L.332, Y.335, H.337, E.339, Y.448, G.474, R.478, G.515, Y.516, G.517, L.518, G.519, R.522, I.533 Ligands: GOL.9 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:E.279, A:S.299, A:Q.301, A:R.322, A:R.322, A:L.332, A:L.332, A:E.339, A:E.339, A:Y.448, A:R.478, A:R.478 Water bridges: A:E.279, A:E.279, A:E.324, A:A.340, A:A.340, A:Y.448, A:G.474 pi-Stacking: A:Y.335, A:Y.335 pi-Cation interactions: A:H.337, A:R.522, A:R.522 ZTE.10: 27 residues within 4Å: Chain B: V.278, E.279, S.299, Q.301, R.322, E.324, R.330, H.331, L.332, Y.335, H.337, E.339, E.341, Y.448, E.471, I.472, G.474, G.475, R.478, G.515, Y.516, G.517, L.518, G.519, R.522, I.533 Ligands: GOL.21 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:E.279, B:S.299, B:R.322, B:R.322, B:L.332, B:L.332, B:E.339, B:R.478, B:R.478, B:R.522 Water bridges: B:E.279, B:E.279, B:A.340, B:A.340, B:Y.448, B:Y.448 pi-Stacking: B:Y.335, B:Y.335 pi-Cation interactions: B:H.337, B:R.522, B:R.522

19 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: M.251, R.254, D.258, S.368, P.369 Ligand excluded by PLIP GOL.3: 1 residues within 4Å: Chain A: F.415 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: R.329, R.425, N.468, T.525, N.529, R.530, Y.531 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: H.403, D.404, V.405, T.430 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: F.261, Y.265, Y.266 Chain B: R.254 Ligand excluded by PLIP GOL.7: 11 residues within 4Å: Chain A: R.249, Q.319, E.334, Y.335, T.336, E.521, C.537, Y.539, R.541 Chain B: T.269, P.271 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: C.359, D.360, D.363, R.386 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: R.322, H.331, E.471, R.522 Ligands: ZTE.1 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain B: L.172, A.211, P.212, A.213 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: M.251, R.254, D.258, S.368 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain B: R.329, N.468, T.525, W.526, N.529, R.530 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain B: P.110, P.112, R.127, Y.182, F.204 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: F.285, A.323, Q.325 Chain B: D.288, Y.289, F.290 Ligand excluded by PLIP GOL.16: 10 residues within 4Å: Chain A: P.271 Chain B: R.249, Q.319, Y.335, T.336, E.521, C.537, L.538, Y.539, R.541 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: C.359, D.360, D.363, R.386 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain B: Y.168, N.169, L.172 Ligands: GOL.19 Ligand excluded by PLIP GOL.19: 2 residues within 4Å: Chain B: L.210 Ligands: GOL.18 Ligand excluded by PLIP GOL.20: 2 residues within 4Å: Chain B: G.122, Y.123 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: R.322, H.331, R.522 Ligands: ZTE.10 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, S.C. et al., Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase. Nat Commun (2024)

Release Date

2024-02-07

Peptides

Asparagine--tRNA ligase, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Asparagine--tRNA ligase, cytoplasmic

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