SMTL ID : 4yye.1

Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex with the canonical tRNAThr and threonyl sulfamoyl adenylate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.131, H.182, H.317 Ligands: TSB.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.131, A:H.182, A:H.317 ZN.6: 4 residues within 4Å: Chain B: C.131, H.182, H.317 Ligands: TSB.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.131, B:H.182, B:H.317

2 x TSB: 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE(Non-covalent)

TSB.2: 22 residues within 4Å: Chain A: M.129, C.131, R.160, E.162, T.171, R.172, L.173, F.176, Q.178, D.180, H.182, Y.268, Q.285, V.286, T.288, Q.290, H.317, R.318, G.322, S.323, R.326 Ligands: ZN.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:T.288 Hydrogen bonds: A:R.160, A:R.160, A:E.162, A:E.162, A:L.173, A:Q.178, A:Q.285, A:Q.285, A:Q.290, A:Q.290, A:S.323, A:S.323, A:R.326 Water bridges: A:N.130, A:D.180 Salt bridges: A:R.160 pi-Stacking: A:F.176, A:F.176 pi-Cation interactions: A:R.326, A:R.326 TSB.7: 22 residues within 4Å: Chain B: M.129, C.131, R.160, E.162, T.171, R.172, L.173, F.176, Q.178, D.180, H.182, Y.268, Q.285, V.286, T.288, Q.290, H.317, R.318, G.322, S.323, R.326 Ligands: ZN.6 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:T.288 Hydrogen bonds: B:R.160, B:R.160, B:E.162, B:R.172, B:L.173, B:Q.178, B:D.180, B:Y.268, B:Q.285, B:Q.285, B:Q.290, B:S.323, B:S.323, B:R.326 Water bridges: B:N.130, B:Q.178 Salt bridges: B:R.160 pi-Stacking: B:F.176, B:F.176 pi-Cation interactions: B:R.326, B:R.326

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

SO4.3: 3 residues within 4Å: Chain A: W.388, I.453, K.457 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.388 Salt bridges: A:K.457 SO4.4: 3 residues within 4Å: Chain A: T.186, P.187, S.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.188, A:S.188, A:S.188 SO4.5: 5 residues within 4Å: Chain A: F.223, N.225, K.259, M.275, T.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.225 Salt bridges: A:K.259 SO4.8: 4 residues within 4Å: Chain B: F.233, I.234, G.235, R.298 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.235, B:R.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holman, K.M. et al., The crystal structure of yeast mitochondrial ThrRS in complex with the canonical threonine tRNA. Nucleic Acids Res. (2016)

Release Date

2016-01-06

Peptides

Threonine--tRNA ligase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Threonine--tRNA ligase, mitochondrial

Related Entries With Identical Sequence