SMTL ID : 2qui.1

Crystal structures of human tryptophanyl-tRNA synthetase in complex with Tryptophanamide and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: W.88, S.165, K.200 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.165

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

LTN.2: 15 residues within 4Å: Chain A: Y.159, T.160, G.161, R.162, G.163, Q.194, T.196, E.199, K.200, Q.284, I.307, C.309, Q.313, F.317 Ligands: ATP.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.159, A:I.307, A:Q.313, A:F.317 Hydrogen bonds: A:Y.159, A:G.163, A:E.199, A:K.200, A:Q.284 Water bridges: A:G.163, A:G.163, A:K.200, A:Q.313, A:Q.313 LTN.4: 14 residues within 4Å: Chain B: Y.159, T.160, G.161, R.162, G.163, Q.194, T.196, E.199, K.200, Q.284, I.307, C.309, Q.313, F.317 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.159, B:I.307, B:Q.313, B:F.317 Hydrogen bonds: B:Y.159, B:G.163, B:E.199, B:K.200, B:Q.284 Water bridges: B:G.163, B:G.163, B:K.200, B:Q.313, B:Q.313

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

ATP.3: 20 residues within 4Å: Chain A: R.162, G.163, S.165, S.166, A.168, H.170, G.172, H.173, A.310, D.312, Q.313, F.339, F.340, K.349, M.350, S.351, A.352, S.353 Ligands: MG.1, LTN.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:S.165, A:S.165, A:S.166, A:D.312, A:Q.313, A:F.340, A:F.340, A:K.349, A:M.350, A:A.352, A:S.353 Water bridges: A:R.162, A:G.163, A:K.200 Salt bridges: A:R.162, A:H.173, A:H.173, A:K.349 pi-Cation interactions: A:K.349

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, N. et al., Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states. Nucleic Acids Res. (2008)

Release Date

2008-04-29

Peptides

Tryptophanyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophanyl-tRNA synthetase

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