SMTL ID : 5xix.1 (1 other biounit)

The canonical domain of human asparaginyl-tRNA synthetase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: L.134 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.134 GOL.2: 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.3: 11 residues within 4Å: Chain A: R.173, Q.243, E.258, Y.259, T.260, E.445, C.461, L.462 Chain B: T.193, P.194, P.195 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.173, A:Q.243, A:Y.259, A:T.260, A:L.462, B:P.194 Water bridges: A:Y.463 GOL.4: 5 residues within 4Å: Chain A: F.268, L.269, T.270, P.436 Chain B: F.55 No protein-ligand interaction detected (PLIP) GOL.5: 5 residues within 4Å: Chain A: Y.92, N.93, L.96, L.131 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.92, A:Y.92, A:N.93 GOL.6: 5 residues within 4Å: Chain A: F.185, Y.189, Y.190 Chain B: R.178, P.293 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.189, B:R.178 GOL.7: 9 residues within 4Å: Chain A: S.223, Q.225, H.261, E.263, G.398, R.402, Y.440, G.441, L.442 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.223, A:Q.225, A:R.402, A:G.441 Water bridges: A:A.264, A:Y.372 GOL.8: 6 residues within 4Å: Chain B: M.175, R.178, D.182, K.291, S.292, P.293 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.178, B:D.182, B:K.291 GOL.9: 4 residues within 4Å: Chain B: E.378, D.379, S.380, R.381 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.378, B:S.380, B:R.381 GOL.10: 10 residues within 4Å: Chain A: T.193, P.194 Chain B: R.173, Q.243, E.258, Y.259, T.260, E.445, C.461, L.462 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.193, B:Q.243, B:L.462 GOL.11: 7 residues within 4Å: Chain A: G.133, L.134 Chain B: F.404, D.405, S.406, R.430, T.434 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.405, B:S.406, A:L.134 Water bridges: B:D.405, B:E.407, B:R.430, A:L.134 GOL.12: 6 residues within 4Å: Chain B: L.96, S.98, L.134, A.135, P.136, A.137 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.96, B:S.98, B:A.135, B:A.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J.S. et al., Unique N-terminal extension domain of human asparaginyl-tRNA synthetase elicits CCR3-mediated chemokine activity. Int. J. Biol. Macromol. (2018)

Release Date

2018-05-02

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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