SMTL ID : 9jc7.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: R.68, H.73, D.75, R.84, H.85, H.86, F.89, M.91, E.173, E.199, I.200, W.201, N.202, G.227, G.229, R.232 Ligands: ALA.2, MLT.9 17 PLIP interactions: 16 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.68, A:D.75, 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:R.232, A.2 Water bridges: A:N.243 Salt bridges: A:R.68, A:R.68 pi-Stacking: A:F.89, A:F.89 ATP.12: 16 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, N.202, G.227, G.229, R.232 Ligands: ALA.13, CIT.16 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: 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.229, B:R.232, B:R.232, A.13 Water bridges: B:N.243 Salt bridges: B:R.68 pi-Stacking: B:F.89, B:F.89 pi-Cation interactions: B:R.232

2 x ALA: ALANINE(Non-covalent)

ALA.2: 8 residues within 4Å: Chain A: A.40, M.42, M.91, W.160, N.202, V.204, D.225 Ligands: ATP.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.204 Hydrogen bonds: A:N.202, A:D.225 Water bridges: A:G.41 ALA.13: 9 residues within 4Å: Chain B: A.40, M.42, M.91, N.202, V.204, D.225, T.226, G.227 Ligands: ATP.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.204 Hydrogen bonds: B:N.202, B:N.202 Water bridges: B:M.42, B:M.42

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: S.26, V.28, G.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.26, A:V.28 EDO.4: 4 residues within 4Å: Chain A: G.294, Y.297, V.298, R.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.294, A:R.301 EDO.5: 5 residues within 4Å: Chain A: P.23, S.24, S.63, A.334, Y.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.24 EDO.6: 3 residues within 4Å: Chain A: A.155, F.159, A.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.155, A:A.161 EDO.8: 5 residues within 4Å: Chain A: Y.100, F.101, K.102, R.103, D.104 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.101, A:F.101, A:R.103, A:R.103, A:D.104 Water bridges: A:K.102 EDO.10: 5 residues within 4Å: Chain A: F.129, D.130, E.131, G.154, A.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.131, A:A.155 Water bridges: A:G.154 EDO.11: 5 residues within 4Å: Chain A: F.13, R.17, N.107, F.108, D.111 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.17, A:R.17, A:D.111 Water bridges: A:N.107 EDO.17: 5 residues within 4Å: Chain B: P.23, S.24, S.63, A.334, Y.335 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.24 EDO.18: 5 residues within 4Å: Chain B: Y.100, F.101, K.102, R.103, D.104 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.101, B:F.101, B:R.103, B:R.103, B:D.104 Water bridges: B:K.102 EDO.19: 8 residues within 4Å: Chain B: L.76, V.79, V.272, H.276, R.305, H.309, D.400, R.403 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.79, B:R.305, B:R.305, B:R.403 EDO.20: 5 residues within 4Å: Chain B: D.317, T.318, Y.321, K.322, K.350 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.321, B:Y.321, B:K.322, B:K.350 EDO.21: 5 residues within 4Å: Chain B: L.259, G.314, I.315, Q.316, D.317 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.314, B:Q.316, B:D.317, B:D.317 EDO.22: 5 residues within 4Å: Chain B: P.380, G.381, D.382, G.413, E.417 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.381, B:D.382 EDO.23: 5 residues within 4Å: Chain B: F.13, R.17, N.107, F.108, D.111 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.17, B:R.17, B:D.111 Water bridges: B:N.107 EDO.24: 4 residues within 4Å: Chain B: I.307, I.315, T.318, E.353 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.315 Water bridges: B:E.353

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 5 residues within 4Å: Chain A: I.315, D.317, T.318, F.319, K.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.259 FMT.14: 5 residues within 4Å: Chain B: Y.244, E.245, V.253, L.265, R.271 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.271 FMT.15: 3 residues within 4Å: Chain B: Q.44, E.53, V.55 No protein-ligand interaction detected (PLIP)

1 x MLT: D-MALATE(Non-covalent)

MLT.9: 7 residues within 4Å: Chain A: R.68, D.75, R.84, H.85, E.199, R.232 Ligands: ATP.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.232 Water bridges: A:R.84, A:H.85, A:E.199 Salt bridges: A:R.68, A:R.84, A:H.85, A:H.85, A:R.232, A:R.232

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

CIT.16: 7 residues within 4Å: Chain B: R.68, D.75, R.84, H.85, E.199, R.232 Ligands: ATP.12 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.199, B:R.232, B:R.232 Salt bridges: B:R.68, B:R.84, B:R.84, B:H.85, B:H.85, B:R.232

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