SMTL ID : 4bw9.1

PylRS Y306G, Y384F, I405R mutant in complex with AMP-PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.233, S.236 Ligands: ANP.3, EDO.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.233, A:S.236, H2O.2, H2O.2 MG.2: 3 residues within 4Å: Chain A: R.167, H.175 Ligands: ANP.3 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain B: E.233, S.236 Ligands: ANP.11, EDO.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.233, B:S.236, H2O.4, H2O.4 MG.10: 3 residues within 4Å: Chain B: R.167, H.175 Ligands: ANP.11 No protein-ligand interaction detected (PLIP)

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 20 residues within 4Å: Chain A: R.167, E.169, E.174, 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, 1PE.4, EDO.7, EDO.8 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.167, A:E.169, A:E.169, A:L.176, A:E.233, A:E.233, A:E.233, A:E.233, A:S.236, A:S.236, A:G.260, A:R.263, A:R.263 Water bridges: A:Q.124 Salt bridges: A:R.167 pi-Stacking: A:F.179, A:F.179 pi-Cation interactions: A:R.263, A:R.263 ANP.11: 20 residues within 4Å: Chain B: R.167, E.169, E.174, 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.9, MG.10, 1PE.12, EDO.15, EDO.16 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.167, B:E.169, B:E.169, B:L.176, B:E.233, B:E.233, B:E.233, B:E.233, B:S.236, B:S.236, B:G.260, B:R.263, B:R.263 Water bridges: B:Q.124 Salt bridges: B:R.167 pi-Stacking: B:F.179, B:F.179 pi-Cation interactions: B:R.263, B:R.263

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 8 residues within 4Å: Chain A: M.137, A.139, N.183, S.236, W.254, G.256, A.257 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.183 1PE.12: 8 residues within 4Å: Chain B: M.137, A.139, N.183, S.236, W.254, G.256, A.257 Ligands: ANP.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.183

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

EDO.5: 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.6: 8 residues within 4Å: Chain A: N.78, R.276, A.277, A.278, Y.283, Y.284, N.285, G.286 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.78, A:R.276, A:N.285, A:G.286 EDO.7: 5 residues within 4Å: Chain A: D.216, D.226, E.233 Ligands: MG.1, ANP.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.216, A:D.216 EDO.8: 6 residues within 4Å: Chain A: H.175, D.231, L.232, E.233, R.263 Ligands: ANP.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.13: 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.14: 8 residues within 4Å: Chain B: N.78, R.276, A.277, A.278, Y.283, Y.284, N.285, G.286 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.78, B:R.276, B:N.285, B:G.286 EDO.15: 5 residues within 4Å: Chain B: D.216, D.226, E.233 Ligands: MG.9, ANP.11 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.216, B:D.216 EDO.16: 6 residues within 4Å: Chain B: H.175, D.231, L.232, E.233, R.263 Ligands: ANP.11 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

Schneider, S. et al., Structural Insights Into Incorporation of Norbornene Amino Acids for Click Modification of Proteins. Chem.Bio.Chem. (2013)

Release Date

2013-07-31

Peptides

PYRROLYSINE--TRNA LIGASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PYRROLYSINE--TRNA LIGASE

Related Entries With Identical Sequence