SMTL ID : 3ugq.1

Crystal structure of the apo form of the yeast mitochondrial threonyl-tRNA synthetase determined at 2.1 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.131, H.182, Y.268, H.317 Ligands: K.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.131, A:H.182, A:H.317 ZN.12: 5 residues within 4Å: Chain B: C.131, H.182, Y.268, H.317 Ligands: K.20 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.131, B:H.182, B:H.317

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

SO4.2: 2 residues within 4Å: Chain A: P.149, R.151 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.151, A:R.151 Salt bridges: A:R.151 SO4.3: 6 residues within 4Å: Chain A: M.129, R.160, K.271, Q.285, Q.290 Ligands: K.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.285, A:Q.290 Water bridges: A:K.271, A:K.271 Salt bridges: A:R.160, A:K.271 SO4.4: 1 residues within 4Å: Chain A: R.229 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.229, A:R.229, A:E.244 Salt bridges: A:R.229 SO4.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.6: 4 residues within 4Å: Chain A: F.223, N.225, K.259, T.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.225 Salt bridges: A:K.259 SO4.7: 5 residues within 4Å: Chain A: E.99, G.102, N.106, I.234, R.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.106 Water bridges: A:R.298, A:R.298 Salt bridges: A:R.298 SO4.13: 2 residues within 4Å: Chain B: P.149, R.151 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.151, B:R.151 Salt bridges: B:R.151 SO4.14: 6 residues within 4Å: Chain B: M.129, R.160, K.271, Q.285, Q.290 Ligands: K.20 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.285, B:Q.290 Water bridges: B:K.271, B:K.271 Salt bridges: B:R.160, B:K.271 SO4.15: 1 residues within 4Å: Chain B: R.229 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.229, B:R.229, B:E.244 Salt bridges: B:R.229 SO4.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.17: 4 residues within 4Å: Chain B: F.223, N.225, K.259, T.283 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.225, B:T.283 Salt bridges: B:K.259 SO4.18: 5 residues within 4Å: Chain B: E.99, G.102, N.106, I.234, R.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.106 Water bridges: B:R.298, B:R.298 Salt bridges: B:R.298

8 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.9: 4 residues within 4Å: Chain A: Q.178, Q.290 Ligands: ZN.1, SO4.3 No protein-ligand interaction detected (PLIP) K.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.11: 1 residues within 4Å: Chain A: K.442 No protein-ligand interaction detected (PLIP) K.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.20: 4 residues within 4Å: Chain B: Q.178, Q.290 Ligands: ZN.12, SO4.14 No protein-ligand interaction detected (PLIP) K.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.22: 1 residues within 4Å: Chain B: K.442 No protein-ligand interaction detected (PLIP)

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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