SMTL ID : 2azx.1 (1 other biounit)

Charged and uncharged tRNAs adopt distinct conformations when complexed with human tryptophanyl-tRNA synthetase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain B: H.170, H.173, K.349, M.350, S.351, A.352, S.353 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.352, B:S.353 Salt bridges: B:H.170, B:H.173, B:K.349 SO4.2: 5 residues within 4Å: Chain B: H.140, D.142, M.143, N.144, Q.145 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.142, B:D.142, B:N.144, B:N.144, B:Q.145, B:Q.145 SO4.3: 4 residues within 4Å: Chain B: D.354, P.355, N.356, F.360 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.356 SO4.4: 4 residues within 4Å: Chain B: T.207, L.208, D.209 Chain D: K.253 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Salt bridges: D:K.253 Hydrogen bonds: B:L.208, B:D.209 SO4.7: 7 residues within 4Å: Chain D: H.170, H.173, K.349, M.350, S.351, A.352, S.353 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.352, D:S.353 Salt bridges: D:H.170, D:H.173, D:K.349 SO4.8: 5 residues within 4Å: Chain D: H.140, D.142, M.143, N.144, Q.145 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.142, D:D.142, D:N.144, D:N.144, D:Q.145, D:Q.145 SO4.9: 4 residues within 4Å: Chain D: D.354, P.355, N.356, F.360 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.356 SO4.10: 4 residues within 4Å: Chain B: K.253 Chain D: T.207, L.208, D.209 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:L.208, D:D.209 Salt bridges: B:K.253

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.5: 13 residues within 4Å: Chain B: Y.159, T.160, G.161, R.162, G.163, Q.194, T.196, E.199, Q.284, I.307, C.309, Q.313, F.317 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:Y.159, B:I.307, B:F.317 Hydrogen bonds: B:Y.159, B:G.163, B:Q.284, B:Q.284 Salt bridges: B:K.200 TRP.6: 8 residues within 4Å: Chain B: L.174, I.178, F.406, E.408, L.441, I.442, H.445, R.448 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.174, B:I.178, B:F.406, B:L.441, B:L.441, B:I.442 Hydrogen bonds: B:H.445, B:R.448 Salt bridges: B:H.130 TRP.11: 13 residues within 4Å: Chain D: Y.159, T.160, G.161, R.162, G.163, Q.194, T.196, E.199, Q.284, I.307, C.309, Q.313, F.317 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:Y.159, D:I.307, D:F.317 Hydrogen bonds: D:Y.159, D:Y.159, D:G.163, D:Q.284, D:Q.284 Salt bridges: D:K.200 TRP.12: 8 residues within 4Å: Chain D: L.174, I.178, F.406, E.408, L.441, I.442, H.445, R.448 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:L.174, D:I.178, D:F.406, D:L.441, D:L.441, D:I.442 Hydrogen bonds: D:H.445, D:R.448 Salt bridges: D:H.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X.L. et al., Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis. Embo J. (2006)

Release Date

2006-08-01

Peptides

Tryptophanyl-tRNA synthetase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

D
A

Tryptophanyl-tRNA synthetase

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