SMTL ID : 3uh0.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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.4: 4 residues within 4Å: Chain B: C.131, H.182, H.317 Ligands: TSB.5 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: 21 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, G.322, S.323, R.326 Ligands: ZN.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:T.288 Hydrogen bonds: A:R.160, A:R.160, A:E.162, A:L.173, A:Q.178, A:Y.268, A:Q.285, A:Q.285, A:Q.290, A:Q.290, A:R.318, A:S.323, A:S.323, A:R.326 Water bridges: A:N.130, A:R.172, A:R.172, A:D.180, A:K.271 Salt bridges: A:R.160, A:K.271 pi-Stacking: A:F.176, A:F.176 pi-Cation interactions: A:R.326, A:R.326 TSB.5: 21 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, G.322, S.323, R.326 Ligands: ZN.4 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:T.288 Hydrogen bonds: B:R.160, B:R.160, B:E.162, B:L.173, B:Q.178, B:Q.285, B:Q.285, B:Q.290, B:Q.290, B:R.318, B:S.323, B:S.323, B:R.326 Water bridges: B:Y.107, B:N.130, B:R.172, B:R.172, B:D.180, B:K.271 Salt bridges: B:R.160, B:K.271 pi-Stacking: B:F.176, B:F.176 pi-Cation interactions: B:R.326, B:R.326

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

SO4.3: 3 residues within 4Å: Chain A: F.440, E.441, K.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.442 Salt bridges: A:K.442 SO4.6: 3 residues within 4Å: Chain B: F.440, E.441, K.442 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.442 Salt bridges: B:K.442

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ling, J. et al., Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-02-22

Peptides

Threonyl-tRNA synthetase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Threonyl-tRNA synthetase, mitochondrial

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