SMTL ID : 3kt6.2 (1 other biounit)

Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with Trp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 14 residues within 4Å: Chain A: Y.106, T.107, G.108, R.109, G.110, E.141, T.143, E.146, K.147, Q.230, I.253, C.255, Q.259, F.263 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:Y.106, A:I.253, A:Q.259, A:F.263 Hydrogen bonds: A:Y.106, A:Y.106, A:G.110, A:E.141, A:Q.230, A:Q.230 Salt bridges: A:K.147 TRP.5: 14 residues within 4Å: Chain B: Y.106, T.107, G.108, R.109, G.110, E.141, T.143, E.146, K.147, Q.230, I.253, C.255, Q.259, F.263 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:Y.106, B:I.253, B:Q.259, B:F.263, B:F.263 Hydrogen bonds: B:Y.106, B:Y.106, B:G.110, B:T.143, B:Q.230, B:Q.230 Salt bridges: B:K.147

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

SO4.2: 8 residues within 4Å: Chain A: R.109, S.112, H.117, H.120, K.295, M.296, S.297, A.298 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.112, A:A.298 Salt bridges: A:R.109, A:H.117, A:H.120, A:K.295 SO4.3: 2 residues within 4Å: Chain A: R.73, E.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.74 Salt bridges: A:R.73 SO4.4: 5 residues within 4Å: Chain A: F.148, T.155, I.156 Chain B: R.199, R.202 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.202, A:I.156 Salt bridges: B:R.199 SO4.6: 6 residues within 4Å: Chain B: R.109, S.112, H.117, H.120, S.297, A.298 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.112, B:S.297 Salt bridges: B:R.109, B:H.117, B:H.120 SO4.7: 4 residues within 4Å: Chain A: R.199 Chain B: F.148, T.155, I.156 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:R.202 Salt bridges: A:R.199 Hydrogen bonds: B:T.155, B:I.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, M. et al., Crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase: new insights into the mechanism of tryptophan activation and implications for anti-fungal drug design. Nucleic Acids Res. (2010)

Release Date

2010-02-16

Peptides

Tryptophanyl-tRNA synthetase, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Tryptophanyl-tRNA synthetase, cytoplasmic

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