SMTL ID : 8tc7.2 (1 other biounit)

Human asparaginyl-tRNA synthetase, apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: L.77, L.115, A.116, P.117, A.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.77, A:A.116, A:A.118 GOL.2: 4 residues within 4Å: Chain A: E.359, D.360, S.361, R.362 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.361, A:S.361 Water bridges: A:S.361, A:S.361, A:S.361, A:R.362 GOL.3: 3 residues within 4Å: Chain A: N.136, N.137 Chain B: Y.405 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.137, A:N.137 Water bridges: A:N.136 GOL.4: 3 residues within 4Å: Chain A: Y.73, N.74, L.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.73, A:N.74 GOL.5: 5 residues within 4Å: Chain A: H.40, R.41, Y.60, P.100, E.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.145 GOL.6: 2 residues within 4Å: Chain A: P.100, G.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.101 GOL.7: 5 residues within 4Å: Chain A: M.156, R.159, D.163, S.273, P.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.159, A:R.159 GOL.8: 5 residues within 4Å: Chain A: H.308, D.309, V.310, L.331, T.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.308, A:D.309, A:T.335 GOL.9: 11 residues within 4Å: Chain A: R.154, Q.224, E.239, Y.240, T.241, E.426, C.442, L.443, Y.444 Chain B: T.174, P.176 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.154, A:Q.224, A:E.239, A:L.443, A:Y.444 GOL.11: 3 residues within 4Å: Chain B: Y.73, N.74, L.77 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.73, B:N.74 Water bridges: B:N.74, B:N.74 GOL.12: 4 residues within 4Å: Chain B: M.156, R.159, D.163, S.273 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.159, B:R.159 GOL.13: 9 residues within 4Å: Chain A: T.174 Chain B: R.154, Q.224, E.239, Y.240, T.241, E.426, C.442, L.443 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.174, B:Q.224, B:T.241, B:L.443 Water bridges: A:T.174, A:T.174, B:Y.444

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 1 residues within 4Å: Chain A: R.32 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: R.32 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
B

B
C

Asparagine--tRNA ligase, cytoplasmic

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