SMTL ID : 8h53.2 (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: 26 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, G.399, R.402, Y.440, G.441, G.443, R.446, I.457 Ligands: 2PN.2, MG.10 22 PLIP interactions: 22 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.443 Water bridges: A:Y.440, A:Y.440 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.11: 26 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, Y.440, G.441, G.443, R.446, I.457 Ligands: 2PN.12, MG.20 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:E.203, B:S.223, B:E.248, B:L.256, B:Y.259, B:I.396, B:V.397, B:G.398, B:R.402, B:R.402, 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.9, MG.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.254, A:H.255, A:E.395, A:R.446, A:R.446 Water bridges: A:D.342 2PN.12: 7 residues within 4Å: Chain B: R.254, H.255, E.395, R.446 Ligands: 4AD.11, MG.19, MG.20 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.254, B:R.446, B:R.446 Water bridges: B:D.342, B:D.342, B:D.387

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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:E.378, A:S.380, A:R.381 GOL.4: 6 residues within 4Å: Chain A: M.175, R.178, C.179, D.182, S.292, P.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.178, A:D.182 GOL.5: 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.6: 4 residues within 4Å: Chain A: H.327, V.329, L.350, T.354 No protein-ligand interaction detected (PLIP) GOL.7: 12 residues within 4Å: Chain A: R.173, Q.243, E.258, Y.259, T.260, E.445, C.461, L.462, Y.463 Chain B: T.193, P.194, P.195 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.173, A:R.173, A:Q.243, A:Q.243, A:L.462, A:Y.463 Water bridges: A:Y.463, A:Y.463 GOL.8: 6 residues within 4Å: Chain A: F.185, G.188, Y.189, Y.190 Chain B: M.175, R.178 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.178, B:R.178, A:F.185 GOL.13: 5 residues within 4Å: Chain B: M.175, R.178, D.182, S.292, P.293 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.178, B:D.182 Water bridges: B:R.178 GOL.14: 3 residues within 4Å: Chain B: Y.92, N.93, L.96 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.92, B:N.93, B:N.93 Water bridges: B:Y.92 GOL.15: 4 residues within 4Å: Chain B: L.96, A.135, P.136, A.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.96, B:A.135, B:A.137 GOL.16: 11 residues within 4Å: Chain A: P.195 Chain B: Q.243, L.256, E.258, Y.259, T.260, E.445, C.461, Y.463, P.464, R.465 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.243, B:T.260, B:T.260, B:R.465, B:R.465 Water bridges: B:Y.463, A:T.193 GOL.17: 5 residues within 4Å: Chain A: R.178 Chain B: F.185, G.188, Y.189, Y.190 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.185, B:Y.189, A:R.178, A:R.178 GOL.18: 4 residues within 4Å: Chain B: P.36, R.51, Y.106, F.128 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.51, B:R.51, B:Y.106, B:Y.106

4 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain A: E.348 Ligands: 2PN.2 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: E.395 Ligands: 4AD.1, 2PN.2 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:E.395, A:E.395, 4AD.1, H2O.3 MG.19: 4 residues within 4Å: Chain B: R.254, E.348, E.395 Ligands: 2PN.12 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain B: E.395 Ligands: 4AD.11, 2PN.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.395, B:E.395, H2O.10

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
B

B
C

Asparagine--tRNA ligase, cytoplasmic

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