SMTL ID : 1mau.1

Crystal structure of Tryptophanyl-tRNA Synthetase Complexed with ATP and Tryptophanamide in a Pre-Transition state Conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: Q.30, Y.33, Q.74 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.33 NA.9: 4 residues within 4Å: Chain B: Q.30, Y.33, Q.74 Ligands: GOL.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.74

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.9, K.111 Ligands: ATP.3, LTN.4 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: Q.9, K.111 Ligands: ATP.11, LTN.12 No protein-ligand interaction detected (PLIP)

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

ATP.3: 25 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.2, LTN.4, CIT.5 25 PLIP interactions: 25 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:D.146, A:I.183, A:K.192, A:M.193, A:M.193, A:K.195, A:S.196, A:S.196 Water bridges: A:N.18, A:P.142, A:E.145, A:S.194, A:S.196 Salt bridges: A:K.111, A:K.192, A:K.192, A:K.195, A:K.195, A:K.195 ATP.11: 25 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.10, LTN.12, CIT.13 25 PLIP interactions: 25 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:D.146, B:I.183, B:K.192, B:M.193, B:M.193, B:K.195, B:S.196, B:S.196 Water bridges: B:N.18, B:P.142, B:E.145, B:S.194, B:S.196 Salt bridges: B:K.111, B:K.192, B:K.192, B:K.195, B:K.195, B:K.195

2 x LTN: L-TRYPTOPHANAMIDE(Non-covalent)

LTN.4: 15 residues within 4Å: Chain A: F.5, S.6, G.7, Q.9, V.40, H.43, Q.107, Y.125, M.129, D.132, I.133, V.141, Q.147 Ligands: MG.2, ATP.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.5, A:F.5, A:D.132, A:I.133, A:V.141 Hydrogen bonds: A:Q.9, A:Y.125 LTN.12: 15 residues within 4Å: Chain B: F.5, S.6, G.7, Q.9, V.40, H.43, Q.107, Y.125, M.129, D.132, I.133, V.141, Q.147 Ligands: MG.10, ATP.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.5, B:F.5, B:D.132, B:I.133, B:V.141 Hydrogen bonds: B:Q.9, B:Y.125, B:Y.125, B:D.132

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

CIT.5: 8 residues within 4Å: Chain A: S.11, G.12, V.47, W.48, Q.49, D.50, S.196 Ligands: ATP.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.11, A:Q.49, A:Q.49, A:D.50, A:S.196, A:S.196 Water bridges: A:Q.9, A:E.53, A:N.57, A:N.57, A:K.111 CIT.13: 8 residues within 4Å: Chain B: S.11, G.12, V.47, W.48, Q.49, D.50, S.196 Ligands: ATP.11 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.11, B:Q.49, B:Q.49, B:D.50, B:S.196, B:S.196 Water bridges: B:Q.9, B:N.57, B:N.57, B:K.111

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: K.218, T.222, Y.265, G.266, K.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.222 GOL.7: 9 residues within 4Å: Chain A: N.34, C.35, Y.36, T.73, Q.74, A.75, T.76, K.306 Ligands: NA.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.34, A:C.35, A:T.73, A:Q.74, A:K.306 GOL.8: 3 residues within 4Å: Chain A: L.248, E.278, T.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.248 GOL.14: 5 residues within 4Å: Chain B: K.218, T.222, Y.265, G.266, K.269 No protein-ligand interaction detected (PLIP) GOL.15: 9 residues within 4Å: Chain B: N.34, C.35, Y.36, T.73, Q.74, A.75, T.76, K.306 Ligands: NA.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.34, B:C.35, B:T.73, B:Q.74, B:T.76, B:K.306 GOL.16: 3 residues within 4Å: Chain B: L.248, E.278, T.279 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.248

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

2003-01-07

Peptides

tryptophan-tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

tryptophan-tRNA ligase

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