SMTL ID : 5ujj.1

Crystal structure of human H130R tryptophanyl-tRNA synthetase in complex with TrpAMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x TYM: TRYPTOPHANYL-5'AMP(Non-covalent)

TYM.1: 27 residues within 4Å: Chain A: Y.159, T.160, G.161, R.162, G.163, G.172, H.173, P.176, Q.194, T.196, E.199, K.200, Q.284, I.307, P.308, C.309, A.310, D.312, Q.313, F.317, T.338, F.339, F.340, K.349, M.350 Ligands: MG.2, MG.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.159, A:I.307, A:Q.313, A:F.317, A:F.317 Hydrogen bonds: A:Y.159, A:G.163, A:Q.284, A:Q.284, A:A.310, A:D.312, A:Q.313, A:F.340, A:F.340, A:M.350 Water bridges: A:G.161, A:R.162, A:R.162 Salt bridges: A:R.162, A:H.173, A:K.200 TYM.4: 26 residues within 4Å: Chain B: Y.159, T.160, G.161, R.162, G.163, G.172, H.173, P.176, Q.194, T.196, E.199, K.200, Q.284, I.307, P.308, C.309, A.310, D.312, Q.313, F.317, T.338, F.339, F.340, K.349, M.350 Ligands: MG.5 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.159, B:I.307, B:Q.313, B:F.317, B:F.317 Hydrogen bonds: B:Y.159, B:Y.159, B:G.163, B:Q.284, B:Q.284, B:A.310, B:D.312, B:F.340, B:F.340, B:K.349, B:M.350 Water bridges: B:G.161, B:Q.313, B:Q.313 Salt bridges: B:R.162, B:K.200

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: K.200 Ligands: TYM.1, MG.3 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: TYM.1, H2O.2 MG.3: 6 residues within 4Å: Chain A: R.162, G.163, S.165, K.200 Ligands: TYM.1, MG.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.163, A:S.165 MG.5: 5 residues within 4Å: Chain B: P.87, D.312, Q.313, K.349 Ligands: TYM.4 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.312, TYM.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, X. et al., An alternative conformation of human TrpRS suggests a role of zinc in activating non-enzymatic function. RNA Biol (2018)

Release Date

2018-01-17

Peptides

Tryptophan--tRNA ligase, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan--tRNA ligase, cytoplasmic