SMTL ID : 9qrp.1

Thermus thermophilus seryl-tRNA synthetase bound to tRNA(ser)(GGA) and seryl-adenylate analogue.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

SSA.1: 20 residues within 4Å: Chain A: T.225, E.227, R.256, A.259, M.270, R.271, V.272, F.275, K.277, E.279, E.345, T.346, H.347, S.348, N.378, N.379, T.380, A.383, P.385, R.386 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:T.225, A:T.225, A:R.256, A:V.272, A:V.272, A:K.277, A:E.345, A:E.345, A:T.346, A:T.380, A:T.380 Water bridges: A:H.204, A:H.204, A:R.271, A:R.271, A:S.350, A:A.383 Salt bridges: A:R.256 pi-Stacking: A:F.275, A:F.275 pi-Cation interactions: A:R.386, A:R.386 SSA.5: 20 residues within 4Å: Chain B: T.225, E.227, R.256, E.258, M.270, R.271, V.272, F.275, K.277, E.279, E.345, T.346, H.347, S.348, N.378, N.379, T.380, A.383, P.385, R.386 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.225, B:R.256, B:E.258, B:V.272, B:E.279, B:T.346, B:T.380, B:T.380 Water bridges: B:H.347, B:S.348, B:A.383, B:A.383 Salt bridges: B:R.256 pi-Stacking: B:F.275, B:F.275 pi-Cation interactions: B:R.386, B:R.386

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

SO4.2: 4 residues within 4Å: Chain A: R.195 Chain B: S.151, G.155, S.156 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.156 Salt bridges: A:R.195 SO4.3: 4 residues within 4Å: Chain A: M.270, R.344, E.345, R.386 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.345 Water bridges: A:R.386 Salt bridges: A:R.344, A:R.386 SO4.4: 4 residues within 4Å: Chain A: Q.152 Chain C: G.7, G.67, C.85 No protein-ligand interaction detected (PLIP) SO4.6: 4 residues within 4Å: Chain B: A.259, G.260, S.261, F.262 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.260, B:G.260, B:F.262 SO4.7: 3 residues within 4Å: Chain B: D.135, V.137, R.267 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.135 Water bridges: B:S.339 Salt bridges: B:R.267 SO4.8: 1 residues within 4Å: Chain B: R.314 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.314 SO4.9: 2 residues within 4Å: Chain B: R.209, Y.221 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.221 Salt bridges: B:R.209 SO4.10: 6 residues within 4Å: Chain B: G.184, F.185, L.186, P.245, L.246, R.247 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.184, B:L.186, B:R.247 SO4.11: 6 residues within 4Å: Chain A: R.149 Chain B: H.234, L.239, P.240, A.243, L.246 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.234, A:R.149 SO4.12: 5 residues within 4Å: Chain B: R.358, R.370, V.371, R.372, Y.373 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.373 Water bridges: B:D.354 Salt bridges: B:R.358, B:R.370

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.13: 3 residues within 4Å: Chain A: E.258, S.261 Chain C: G.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cusack, S. et al., The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site. EMBO J (1996)

Release Date

2025-05-14

Peptides

Serine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine--tRNA ligase

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