SMTL ID : 1m83.1

Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in a Closed, Pre-transition State Conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: Q.9 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: Q.9 Ligands: ATP.7 No protein-ligand interaction detected (PLIP)

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

ATP.2: 23 residues within 4Å: Chain A: G.7, I.8, Q.9, S.11, G.17, N.18, G.21, A.22, K.111, V.143, G.144, D.146, Q.147, G.180, A.181, R.182, I.183, K.192, M.193, S.194, K.195, S.196 Ligands: MG.1 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:Q.9, A:Q.9, A:Q.9, A:S.11, A:N.18, A:G.21, A:P.142, A:I.183, A:K.192, A:M.193, A:M.193, A:K.195, A:S.196, A:S.196, A:S.196 Water bridges: A:N.18, A:K.111, A:K.111, A:S.194, A:S.194 Salt bridges: A:K.111, A:K.192, A:K.192, A:K.195, A:K.195, A:K.195 ATP.7: 23 residues within 4Å: Chain B: G.7, I.8, Q.9, S.11, G.17, N.18, G.21, A.22, K.111, V.143, G.144, D.146, Q.147, G.180, A.181, R.182, I.183, K.192, M.193, S.194, K.195, S.196 Ligands: MG.6 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:Q.9, B:Q.9, B:Q.9, B:S.11, B:N.18, B:G.21, B:P.142, B:I.183, B:K.192, B:M.193, B:M.193, B:K.195, B:S.196, B:S.196, B:S.196 Water bridges: B:N.18, B:K.111, B:K.111, B:S.194, B:S.194 Salt bridges: B:K.111, B:K.192, B:K.192, B:K.195, B:K.195, B:K.195

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: S.11, V.47, W.48, Q.49, D.50, S.196 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.48, A:Q.49, A:D.50 Water bridges: A:N.57 GOL.4: 5 residues within 4Å: Chain A: K.218, T.222, Y.265, G.266, K.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.222 Water bridges: A:K.218, A:G.266 GOL.5: 8 residues within 4Å: Chain A: N.34, C.35, Y.36, T.73, Q.74, A.75, T.76, K.306 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.35, A:T.73, A:Q.74, A:K.306 GOL.8: 6 residues within 4Å: Chain B: S.11, V.47, W.48, Q.49, D.50, S.196 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.48, B:Q.49, B:D.50 Water bridges: B:N.57 GOL.9: 5 residues within 4Å: Chain B: K.218, T.222, Y.265, G.266, K.269 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.218, B:G.266 GOL.10: 8 residues within 4Å: Chain B: N.34, C.35, Y.36, T.73, Q.74, A.75, T.76, K.306 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.35, B:T.73, B:Q.74, B:T.76, B:K.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Retailleau, P. et al., Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations. J.Mol.Biol. (2003)

Release Date

2002-12-18

Peptides

Tryptophan-tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tryptophan-tRNA ligase

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