SMTL ID : 9jdn.1

Crystal structure of alanyl-tRNA synthetase L219M mutant in complex with ATP and L-alanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 18 residues within 4Å: Chain A: R.68, D.75, R.84, H.85, H.86, F.89, M.91, D.157, E.173, E.199, I.200, W.201, N.202, G.227, G.229, R.232 Ligands: ALA.2, TRS.4 14 PLIP interactions: 13 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.68, A:H.86, A:H.86, A:E.199, A:E.199, A:E.199, A:N.202, A:G.229, A:R.232, A.2 Water bridges: A:N.243 Salt bridges: A:R.68 pi-Stacking: A:F.89, A:F.89 ATP.5: 7 residues within 4Å: Chain A: H.241, S.242, Y.244, E.245, L.265, S.266, R.271 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.242, A:S.242, A:E.245, A:R.271 Salt bridges: A:H.241 ATP.6: 18 residues within 4Å: Chain B: R.68, D.75, R.84, H.85, H.86, F.89, M.91, E.173, E.199, I.200, W.201, N.202, G.227, M.228, G.229, R.232 Ligands: ALA.7, TRS.10 18 PLIP interactions: 2 Ligand-Ligand interactions, 16 interactions with chain B Hydrogen bonds: A.7, A.7, B:R.68, B:D.75, B:H.86, B:H.86, B:E.173, B:E.199, B:E.199, B:N.202, B:G.227, B:G.229, B:R.232, B:R.232 Water bridges: B:N.243 Salt bridges: B:R.68 pi-Stacking: B:F.89, B:F.89

2 x ALA: ALANINE(Non-covalent)

ALA.2: 7 residues within 4Å: Chain A: A.40, M.42, M.91, W.160, V.204, D.225 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.204 Water bridges: A:D.225, A:T.226 ALA.7: 7 residues within 4Å: Chain B: A.40, M.42, M.91, W.160, V.204, D.225 Ligands: ATP.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.204 Water bridges: B:M.42, B:D.225

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 7 residues within 4Å: Chain A: V.288, L.289, S.291, E.293, G.294, R.295, G.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.289, A:S.291, A:E.293, A:G.296 CIT.11: 8 residues within 4Å: Chain B: G.287, V.288, L.289, S.291, E.293, G.294, R.295, G.296 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.287, B:L.289, B:S.291, B:G.296

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 5 residues within 4Å: Chain A: R.84, H.85, E.199, R.232 Ligands: ATP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.84, A:R.84, A:E.199, A:R.232, A:R.232 TRS.10: 5 residues within 4Å: Chain B: R.84, H.85, E.199, R.232 Ligands: ATP.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.68, B:R.84, B:R.84, B:E.199, B:R.232, B:R.232

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain B: A.4, R.7, A.8, L.11 Ligands: GOL.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.4, B:R.7, B:R.7 GOL.9: 6 residues within 4Å: Chain B: P.23, S.24, S.63, A.334, Y.335 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.24, B:S.63, B:S.63 GOL.12: 7 residues within 4Å: Chain B: E.77, R.305, V.395, D.396, A.399, D.400, H.411 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.77, B:R.305, B:H.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, W. et al., Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation. Nucleic Acids Res. (2025)

Release Date

2025-06-18

Peptides

Alanine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alanine--tRNA ligase