SMTL ID : 4tqf.1

Crystal Structure of the C-terminal domain of IFRS bound with 2-(5-bromothienyl)-L-Ala and ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.120, R.167, E.169 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: E.233, S.236 Ligands: ATP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.233, A:S.236, H2O.3, H2O.3 MG.12: 4 residues within 4Å: Chain B: E.120, R.167, E.169 Ligands: ATP.14 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain B: E.233, S.236 Ligands: ATP.14 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.233, B:S.236, H2O.5, H2O.5

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

ATP.3: 16 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 Ligands: MG.1, MG.2, EDO.11 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.169, A:L.176, A:E.233, A:S.236, A:G.258, A:G.260, A:R.263 Water bridges: A:Q.124, A:R.167, A:R.167, A:S.236, A:S.236 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.14: 16 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 Ligands: MG.12, MG.13, EDO.22 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:E.169, B:L.176, B:E.233, B:S.236, B:G.258, B:G.260, B:R.263 Water bridges: B:Q.124, B:R.167, B:R.167, 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 33W: 3-(5-bromothiophen-2-yl)-L-alanine(Non-covalent)

33W.4: 9 residues within 4Å: Chain A: M.137, L.138, A.139, M.181, S.183, I.185, W.254, A.257, G.258 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.254 Hydrogen bonds: A:L.138, A:A.139, A:S.183 33W.15: 9 residues within 4Å: Chain B: M.137, L.138, A.139, M.181, S.183, I.185, W.254, A.257, G.258 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.254 Hydrogen bonds: B:L.138, B:A.139, B:S.183

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

EDO.5: 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.6: 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.7: 4 residues within 4Å: Chain A: 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.8: 5 residues within 4Å: Chain A: D.210, K.212, M.228, H.229, G.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.210, A:H.229, A:G.230 EDO.9: 6 residues within 4Å: Chain A: R.147, D.150, G.249, I.250, D.251, K.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.147, A:D.150, A:D.251, A:K.252 EDO.10: 1 residues within 4Å: Chain A: E.194 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain A: E.174, H.175, D.231, L.232, E.233, R.263 Ligands: ATP.3 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.16: 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.17: 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.18: 4 residues within 4Å: Chain B: 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.19: 5 residues within 4Å: Chain B: D.210, K.212, M.228, H.229, G.230 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.210, B:H.229, B:G.230 EDO.20: 6 residues within 4Å: Chain B: R.147, D.150, G.249, I.250, D.251, K.252 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.147, B:D.150, B:D.251, B:K.252 EDO.21: 1 residues within 4Å: Chain B: E.194 No protein-ligand interaction detected (PLIP) EDO.22: 7 residues within 4Å: Chain B: E.174, H.175, D.231, L.232, E.233, R.263 Ligands: ATP.14 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

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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