SMTL ID : 4eo4.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

homo-dimer

Ligands

4 x SSA: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE(Non-covalent)

SSA.1: 21 residues within 4Å: Chain A: M.129, 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.3 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:R.160, A:R.160, A:E.162, A:L.173, A:Q.178, A:Q.178, A:Q.285, A:Q.285, A:Q.290, A:Q.290, A:R.318, A:S.323, A:S.323, A:R.326, A:R.326 Water bridges: A:Y.107, A:R.172, A:R.172 Salt bridges: A:R.160 pi-Stacking: A:F.176, A:F.176 pi-Cation interactions: A:R.326, A:R.326 SSA.2: 8 residues within 4Å: Chain A: V.401, G.402, I.405, K.406, I.409, R.432, R.434, R.437 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.406, A:R.432, A:R.432, A:R.434, A:R.437 pi-Cation interactions: A:R.437, A:R.437 SSA.4: 21 residues within 4Å: Chain B: M.129, R.160, E.162, T.171, R.172, L.173, F.176, Q.178, D.180, H.182, Y.268, K.271, Q.285, V.286, Q.290, H.317, R.318, G.322, S.323, R.326 Ligands: ZN.6 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:R.160, B:R.160, B:E.162, B:L.173, B:Q.178, B:D.180, B:Q.285, B:Q.285, B:Q.290, B:R.318, B:S.323, B:S.323, B:R.326 Water bridges: B:R.172, B:R.172, B:K.271, 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 SSA.5: 8 residues within 4Å: Chain B: V.401, G.402, I.405, K.406, I.409, R.432, R.434, R.437 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.406, B:R.432, B:R.432, B:R.434 pi-Cation interactions: B:R.437, B:R.437

2 x ZN: ZINC ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ling, J. et al., The mechanism of pre-transfer editing in yeast mitochondrial threonyl-tRNA synthetase. J.Biol.Chem. (2012)

Release Date

2012-07-11

Peptides

Threonine--tRNA ligase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Threonine--tRNA ligase, mitochondrial

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