SMTL ID : 6otj.1 (1 other biounit)

Crystal Structure of Tyrosyl-tRNA synthetase from Neisseria gonorrhoeae with bound L-Tyr

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

monomer

Ligands

1 x TYR: TYROSINE(Non-covalent)

TYR.1: 11 residues within 4Å: Chain A: Y.42, G.44, D.46, L.76, T.81, D.86, Y.179, Q.183, D.186, E.199, Q.205 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:L.76, A:Q.183 Hydrogen bonds: A:Y.42, A:D.86, A:Q.183, A:Q.183, A:D.186, A:Q.205 Water bridges: A:D.46

17 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: K.90, A.91, A.92 Ligands: EDO.17 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: T.114, P.115 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: R.64, S.118 Ligand excluded by PLIP SO4.6: 1 residues within 4Å: Chain A: N.251 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: A.268, D.269 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: F.281, L.282, E.310 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: R.64, Q.68, F.281 Ligands: SO4.10 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: R.64, P.115, F.116, S.118 Ligands: SO4.9 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: R.326, R.338 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: T.340, E.341, S.342 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: T.48, H.56, R.94 Ligands: EDO.18 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: T.243, E.244, K.266 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain A: G.246, A.247, W.249 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain A: L.390, N.391, E.416, Y.417, R.419 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain A: T.238, K.239 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain A: Q.23, W.206 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain A: L.282, E.286, V.290, I.306 Ligand excluded by PLIP

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 3 residues within 4Å: Chain A: F.89, S.203, D.204 No protein-ligand interaction detected (PLIP) EDO.11: 3 residues within 4Å: Chain A: G.317, E.318, E.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.318, A:E.319 EDO.15: 2 residues within 4Å: Chain A: R.110, F.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.110, A:R.110 EDO.16: 2 residues within 4Å: Chain A: R.110, N.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.110, A:N.129 EDO.17: 4 residues within 4Å: Chain A: K.90, A.92, R.94 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.92, A:R.94 EDO.18: 6 residues within 4Å: Chain A: H.53, G.55, H.56, K.239 Ligands: SO4.14, EDO.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.239 EDO.19: 4 residues within 4Å: Chain A: M.137, D.141, D.145, Y.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.145, A:Y.185 EDO.22: 3 residues within 4Å: Chain A: P.301, E.302, R.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.305, A:R.305 EDO.25: 6 residues within 4Å: Chain A: H.53, I.54, G.241, A.247, V.248 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal Structure of Tyrosyl-tRNA synthetase from Neisseria gonorrhoeae with bound L-Tyr. to be published

Release Date

2019-05-15

Peptides

Tyrosine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosine--tRNA ligase

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