SMTL ID : 4pbt.1

Crystal structure of the M. jannaschii G2 tRNA synthetase variant bound to 4-trans-cyclooctene-amidopheylalanine (Tco-amF)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.1: 5 residues within 4Å: Chain A: I.63, V.103, D.111, Y.161, K.162 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.103, A:Y.161 Hydrogen bonds: A:K.162 P4G.4: 5 residues within 4Å: Chain B: I.63, V.103, D.111, Y.161, K.162 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.103, B:Y.161 Hydrogen bonds: B:K.162

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: F.35, H.42, G.44, H.45, Q.48, M.205 Ligands: 2LQ.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.48 Water bridges: A:E.36, A:H.45, A:H.45 GOL.5: 7 residues within 4Å: Chain B: F.35, H.42, G.44, H.45, Q.48, M.205 Ligands: 2LQ.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.48 Water bridges: B:E.36, B:H.45, B:H.45

2 x 2LQ: 4-{[(1R,4E)-cyclooct-4-en-1-ylcarbonyl]amino}-L-phenylalanine(Non-covalent)

2LQ.3: 20 residues within 4Å: Chain A: G.32, I.33, G.34, F.35, E.36, I.63, I.64, E.65, A.67, H.70, W.108, I.137, Y.151, Q.155, S.158, I.159, K.162, V.164, Q.173 Ligands: GOL.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.63, A:E.65, A:A.67, A:Q.155, A:K.162, A:V.164 Hydrogen bonds: A:E.65, A:Y.151, A:Q.155, A:Q.155, A:Q.173 Water bridges: A:G.34, A:G.34, A:E.36 pi-Stacking: A:H.70 2LQ.6: 20 residues within 4Å: Chain B: G.32, I.33, G.34, F.35, E.36, I.63, I.64, E.65, A.67, H.70, W.108, I.137, Y.151, Q.155, S.158, I.159, K.162, V.164, Q.173 Ligands: GOL.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.63, B:E.65, B:A.67, B:Q.155, B:K.162, B:V.164 Hydrogen bonds: B:E.65, B:Q.155, B:Q.155, B:Q.173 Water bridges: B:G.34, B:G.34, B:E.36 pi-Stacking: B:H.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cooley, R.B. et al., Gleaning Unexpected Fruits from Hard-Won Synthetases: Probing Principles of Permissivity in Non-canonical Amino Acid-tRNA Synthetases. Chembiochem (2014)

Release Date

2014-07-23

Peptides

Tyrosine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tyrosine--tRNA ligase

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