SMTL ID : 4p3p.1

Structural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Synthetase by Borrelidin 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.94, D.143, H.145, H.271 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.94, A:H.145, A:H.271, H2O.6 ZN.5: 4 residues within 4Å: Chain B: C.94, D.143, H.145, H.271 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.94, B:H.145, B:H.271, H2O.17

2 x 2CR: (1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadeca-4,6-dien-2-yl]cyclopentanecarboxylic acid(Non-covalent)

2CR.2: 14 residues within 4Å: Chain A: T.67, G.68, H.69, N.72, Y.73, M.92, C.94, R.123, Q.141, Y.222, T.242, D.246, L.249, H.271 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:N.72, A:Y.73, A:Y.73, A:Y.222, A:Y.222, A:T.242 Hydrogen bonds: A:Q.141, A:Y.222, A:D.246, A:L.249 Water bridges: A:K.225 Salt bridges: A:R.123 2CR.6: 15 residues within 4Å: Chain B: T.67, G.68, H.69, N.72, Y.73, M.92, C.94, P.95, R.123, Q.141, Y.222, T.242, D.246, L.249, H.271 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.72, B:Y.73, B:Y.73, B:Y.222, B:Y.222, B:T.242 Hydrogen bonds: B:Q.141, B:Y.222, B:D.246, B:L.249 Water bridges: B:R.123 Salt bridges: B:R.123

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: Q.51, I.100, F.101, Q.103, K.106 Chain B: D.12, H.27 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:Q.51, A:Q.51, A:I.100, A:K.106, B:D.12, B:H.27 Water bridges: B:D.12, B:D.12, B:N.28, B:N.28 GOL.4: 8 residues within 4Å: Chain A: V.24, W.26, G.138, T.140, E.279 Chain B: K.54, G.55, P.56 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.24, A:V.24, A:W.26 Water bridges: B:F.57 GOL.7: 3 residues within 4Å: Chain B: W.70, D.71, K.74 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.71, B:K.74 GOL.8: 7 residues within 4Å: Chain A: K.54, G.55, P.56 Chain B: V.24, W.26, T.140, E.279 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.24, B:V.24, B:E.279, B:E.279 Water bridges: B:S.120, B:S.120, B:T.140, B:T.140, A:F.57 GOL.9: 7 residues within 4Å: Chain A: D.12, H.27 Chain B: Q.51, I.100, F.101, Q.103, K.106 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.12, B:Q.51, B:F.101, B:K.106 Water bridges: A:D.12, A:N.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fang, P. et al., Structural basis for full-spectrum inhibition of translational functions on a tRNA synthetase. Nat Commun (2015)

Release Date

2015-03-11

Peptides

Threonine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Threonine--tRNA ligase

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