SMTL ID : 8h53.1 (1 other biounit)

Human asparaginyl-tRNA synthetase in complex with asparagine-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

2 x 4AD: 4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM ADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

4AD.1: 24 residues within 4Å: Chain A: V.202, E.203, S.223, Q.225, R.246, E.248, R.254, H.255, L.256, Y.259, H.261, E.263, Y.372, E.395, I.396, V.397, G.398, R.402, Y.440, G.441, G.443, R.446 Ligands: 2PN.2, MG.13 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:E.203, A:E.203, A:S.223, A:E.248, A:E.248, A:L.256, A:E.263, A:Y.372, A:E.395, A:R.402, A:R.402, A:G.439, A:G.441, A:G.443, A:R.446 Water bridges: A:R.246, A:A.264, A:A.264 Salt bridges: A:R.246, A:R.246, A:H.261 pi-Stacking: A:Y.259, A:Y.259 pi-Cation interactions: A:R.446, A:R.446 4AD.14: 27 residues within 4Å: Chain B: V.202, E.203, S.223, Q.225, R.246, E.248, R.254, H.255, L.256, Y.259, H.261, E.263, Y.372, E.395, I.396, V.397, G.398, G.399, R.402, G.439, Y.440, G.441, G.443, R.446, I.457 Ligands: 2PN.15, MG.22 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:E.203, B:S.223, B:L.256, B:L.256, B:Y.259, B:I.396, B:V.397, B:R.402, B:R.402, B:G.439, B:G.443 Water bridges: B:A.264, B:A.264 Salt bridges: B:R.246, B:R.246, B:H.261 pi-Stacking: B:Y.259, B:Y.259 pi-Cation interactions: B:R.446, B:R.446

2 x 2PN: IMIDODIPHOSPHORIC ACID(Non-covalent)

2PN.2: 7 residues within 4Å: Chain A: R.254, H.255, E.395, R.446 Ligands: 4AD.1, MG.12, MG.13 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.254, A:E.395, A:R.446, A:R.446 Water bridges: A:R.246, A:D.342 2PN.15: 7 residues within 4Å: Chain B: R.254, H.255, E.395, R.446 Ligands: 4AD.14, MG.21, MG.22 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.254, B:R.254, B:H.255, B:E.395, B:R.446, B:R.446 Water bridges: B:E.348, B:K.369, B:D.387, B:E.395

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: M.175, R.178, D.182, S.292, P.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.178, A:R.178 GOL.4: 4 residues within 4Å: Chain A: Y.92, N.93, L.96, L.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.92, A:N.93 GOL.5: 4 residues within 4Å: Chain A: E.378, D.379, S.380, R.381 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.380, A:S.380 Water bridges: A:R.381 GOL.6: 9 residues within 4Å: Chain A: R.173, Q.243, E.258, Y.259, T.260, E.445, C.461, Y.463 Chain B: P.195 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.173, A:R.173, A:Q.243, A:E.445 Water bridges: A:R.173, A:L.462, A:Y.463 GOL.7: 6 residues within 4Å: Chain A: H.59, R.60, V.72, Y.79, P.119, E.164 No protein-ligand interaction detected (PLIP) GOL.8: 5 residues within 4Å: Chain A: H.327, D.328, V.329, L.350, T.354 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.328 GOL.9: 5 residues within 4Å: Chain A: F.185, Y.189, Y.190 Chain B: R.178 Ligands: GOL.19 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.185, A:Y.189, B:R.178 GOL.10: 5 residues within 4Å: Chain A: L.96, S.98, A.135, P.136, A.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.98, A:A.135 GOL.11: 5 residues within 4Å: Chain A: R.178 Chain B: F.185, G.188, Y.189, Y.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.178 GOL.16: 4 residues within 4Å: Chain B: M.175, R.178, D.182, S.292 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.178, B:R.178 GOL.17: 4 residues within 4Å: Chain B: Y.92, N.93, L.96, L.131 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.92, B:Y.92, B:N.93 GOL.18: 13 residues within 4Å: Chain A: T.193, P.195 Chain B: R.173, Q.243, L.256, E.258, Y.259, T.260, E.445, C.461, Y.463, P.464, R.465 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.173, B:Q.243, B:T.260, B:T.260, B:R.465, B:R.465 GOL.19: 6 residues within 4Å: Chain A: Y.190 Chain B: K.171, M.175, P.293, I.297 Ligands: GOL.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:K.171, A:Y.190 GOL.20: 4 residues within 4Å: Chain A: F.55 Chain B: F.268, T.270, P.436 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 2 residues within 4Å: Chain A: E.395 Ligands: 2PN.2 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain A: E.395 Ligands: 4AD.1, 2PN.2 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.395, A:E.395, 4AD.1, H2O.2, H2O.4 MG.21: 3 residues within 4Å: Chain B: D.342, I.343 Ligands: 2PN.15 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain B: E.395 Ligands: 4AD.14, 2PN.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.395, B:E.395, H2O.9, H2O.11

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

2023-10-25

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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