SMTL ID : 4tqd.1

Crystal Structure of the C-terminal domain of IFRS bound with 3-iodo-L-Phe and ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: R.167, H.175 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: D.226, E.233, S.236 Ligands: MG.3, ATP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.233, A:S.236, H2O.3, H2O.5 MG.3: 3 residues within 4Å: Chain A: E.233 Ligands: MG.2, ATP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.233, H2O.5, H2O.5, H2O.5 MG.13: 3 residues within 4Å: Chain B: R.167, H.175 Ligands: ATP.16 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain B: D.226, E.233, S.236 Ligands: MG.15, ATP.16 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.233, B:S.236, H2O.7, H2O.9 MG.15: 3 residues within 4Å: Chain B: E.233 Ligands: MG.14, ATP.16 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.233, H2O.9, H2O.9, H2O.9

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

ATP.4: 19 residues within 4Å: Chain A: R.167, E.169, H.175, L.176, F.179, M.181, E.233, L.234, S.235, S.236, G.258, G.260, R.263, I.274 Ligands: MG.1, MG.2, MG.3, 33S.5, EDO.11 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.169, A:L.176, A:E.233, A:E.233, A:S.236, A:G.260, A:R.263 Water bridges: A:Q.124, A:R.167, A:R.167, A:R.167, A:R.167 Salt bridges: A:R.167, A:R.167, A:H.175, A:R.263 pi-Stacking: A:F.179, A:F.179 pi-Cation interactions: A:R.263, A:R.263 ATP.16: 19 residues within 4Å: Chain B: R.167, E.169, H.175, L.176, F.179, M.181, E.233, L.234, S.235, S.236, G.258, G.260, R.263, I.274 Ligands: MG.13, MG.14, MG.15, 33S.17, EDO.23 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:E.169, B:L.176, B:E.233, B:E.233, B:S.236, B:G.260, B:R.263 Water bridges: B:Q.124, B:R.167, B:R.167, B:R.167, B:R.167, B:E.233, B:S.236, B:S.236, B:S.236 Salt bridges: B:R.167, B:R.167, B:H.175, B:R.263 pi-Stacking: B:F.179, B:F.179 pi-Cation interactions: B:R.263, B:R.263

2 x 33S: 3-iodo-L-phenylalanine(Non-covalent)

33S.5: 11 residues within 4Å: Chain A: M.137, R.167, S.183, I.185, S.236, V.238, W.254, G.256, A.257, G.258 Ligands: ATP.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.238, A:W.254 Salt bridges: A:R.167 33S.17: 11 residues within 4Å: Chain B: M.137, R.167, S.183, I.185, S.236, V.238, W.254, G.256, A.257, G.258 Ligands: ATP.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.238, B:W.254 Salt bridges: B:R.167

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 8 residues within 4Å: Chain A: N.78, R.276, A.277, A.278, Y.283, Y.284, N.285, G.286 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.78, A:N.78, A:R.276, A:N.285, A:G.286 EDO.7: 7 residues within 4Å: Chain A: Y.79, K.82, L.83, E.86, L.265, K.268, H.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.86, A:K.268, A:H.269 EDO.8: 5 residues within 4Å: Chain A: R.89, F.90, D.93, R.94, H.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.94, A:R.94 Water bridges: A:F.90, A:H.206 EDO.9: 5 residues within 4Å: Chain A: D.210, F.211, K.212, H.229, G.230 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.210, A:D.210, A:K.212, A:K.212, A:G.230 EDO.10: 7 residues within 4Å: Chain A: R.147, D.150, M.187, G.249, I.250, D.251, K.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.150, A:D.251, A:D.251 Water bridges: A:D.150 EDO.11: 7 residues within 4Å: Chain A: E.174, H.175, D.231, L.232, E.233, R.263 Ligands: ATP.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.175, A:D.231, A:E.233, A:R.263, A:R.263 EDO.12: 1 residues within 4Å: Chain A: E.194 No protein-ligand interaction detected (PLIP) EDO.18: 8 residues within 4Å: Chain B: N.78, R.276, A.277, A.278, Y.283, Y.284, N.285, G.286 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.78, B:N.78, B:R.276, B:N.285, B:G.286 EDO.19: 7 residues within 4Å: Chain B: Y.79, K.82, L.83, E.86, L.265, K.268, H.269 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.86, B:K.268, B:H.269 EDO.20: 5 residues within 4Å: Chain B: R.89, F.90, D.93, R.94, H.206 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.94, B:R.94 Water bridges: B:F.90, B:H.206 EDO.21: 5 residues within 4Å: Chain B: D.210, F.211, K.212, H.229, G.230 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.210, B:D.210, B:K.212, B:K.212, B:G.230 EDO.22: 7 residues within 4Å: Chain B: R.147, D.150, M.187, G.249, I.250, D.251, K.252 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.150, B:D.251, B:D.251 Water bridges: B:D.150 EDO.23: 7 residues within 4Å: Chain B: E.174, H.175, D.231, L.232, E.233, R.263 Ligands: ATP.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.175, B:D.231, B:E.233, B:R.263, B:R.263 EDO.24: 1 residues within 4Å: Chain B: E.194 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, L.T. et al., Polyspecific pyrrolysyl-tRNA synthetases from directed evolution. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-11-12

Peptides

Pyrrolysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysine--tRNA ligase

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