SMTL ID : 8tc8.1 (1 other biounit)

Human asparaginyl-tRNA synthetase bound to adenosine 5'-sulfamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x NSS: 5'-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE(Non-covalent)

NSS.1: 28 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, A.340, Y.448, E.471, I.472, V.473, G.474, R.478, G.515, Y.516, G.517, L.518, G.519, R.522, I.533 Ligands: GOL.4, NA.8 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:E.279, A:S.299, A:R.322, A:E.324, A:E.324, A:L.332, A:E.339, A:E.339, A:Y.448, A:Y.448, A:R.478, A:R.478, A:G.517, A:G.519, A:R.522, A:R.522 Water bridges: A:E.279, A:E.279, A:R.322, A:A.340, A:A.340, A:Y.448, A:G.474 Salt bridges: A:R.322 pi-Stacking: A:Y.335, A:Y.335 pi-Cation interactions: A:R.522, A:R.522 NSS.9: 29 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, V.473, G.474, G.475, R.478, G.515, Y.516, G.517, L.518, G.519, R.522, I.533 Ligands: GOL.11, NA.12 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:S.299, B:S.299, B:R.322, B:E.324, B:L.332, B:Y.335, B:E.339, B:E.471, B:I.472, B:R.478, B:R.478, B:G.519, B:R.522 Water bridges: B:E.279, B:R.322, B:A.340, B:S.446, B:Y.448, B:Y.448 Salt bridges: B:R.322 pi-Stacking: B:Y.335, B:Y.335 pi-Cation interactions: B:R.522, B:R.522

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Chain A: F.415 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.394, A:S.394 GOL.3: 4 residues within 4Å: Chain A: L.172, A.211, P.212, A.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.171, A:A.213 GOL.4: 6 residues within 4Å: Chain A: E.324, H.331, E.471, R.522 Ligands: NSS.1, NA.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.324, A:E.471, A:E.471, A:R.522, A:R.522 Water bridges: A:R.330 GOL.5: 4 residues within 4Å: Chain A: M.251, R.254, D.258, S.368 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.254 Water bridges: A:R.254, A:R.364 GOL.6: 4 residues within 4Å: Chain A: Y.168, N.169, L.172, L.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.168, A:N.169 Water bridges: A:N.169 GOL.7: 3 residues within 4Å: Chain A: W.399, H.403, V.405 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.430 GOL.10: 4 residues within 4Å: Chain B: M.251, R.254, D.258, S.368 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.254, B:D.258 Water bridges: B:K.367, B:K.367 GOL.11: 7 residues within 4Å: Chain B: E.324, R.330, H.331, E.471, R.522 Ligands: NSS.9, NA.12 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.324, B:R.330, B:E.471, B:E.471, B:R.522, B:R.522 Water bridges: B:E.471

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

NA.8: 3 residues within 4Å: Chain A: E.471 Ligands: NSS.1, GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.471 NA.12: 3 residues within 4Å: Chain B: E.471 Ligands: NSS.9, GOL.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.471 Water bridges: B:K.445

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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