SMTL ID : 4q6g.1

Crystal Structure of the C-terminal domain of AcKRS-1 bound with N-acetyl-lysine and ADPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

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

ANP.1: 15 residues within 4Å: Chain A: R.143, E.145, H.151, L.152, F.155, M.157, E.209, L.210, S.211, S.212, G.234, F.235, G.236, R.239 Ligands: ALY.8 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.143, A:H.151, A:L.152, A:L.152, A:E.209, A:E.209, A:E.209, A:S.212, A:S.212, A:G.236, A:R.239, A:R.239 Salt bridges: A:R.143 pi-Stacking: A:F.155, A:F.155 pi-Cation interactions: A:R.239

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

EDO.2: 8 residues within 4Å: Chain A: N.54, R.252, A.253, A.254, Y.259, Y.260, N.261, G.262 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.54, A:N.54, A:R.252, A:N.261, A:G.262 EDO.3: 7 residues within 4Å: Chain A: Y.55, K.58, L.59, E.62, L.241, K.244, H.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.62, A:K.244, A:H.245 EDO.4: 5 residues within 4Å: Chain A: R.65, F.66, D.69, R.70, H.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.70, A:H.182 EDO.5: 5 residues within 4Å: Chain A: D.186, K.188, M.204, H.205, G.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.186, A:D.186, A:K.188, A:G.206 EDO.6: 7 residues within 4Å: Chain A: R.123, D.126, M.163, G.225, I.226, D.227, K.228 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.123, A:D.126 EDO.7: 1 residues within 4Å: Chain A: E.170 No protein-ligand interaction detected (PLIP)

1 x ALY: N(6)-ACETYLLYSINE(Non-covalent)

ALY.8: 14 residues within 4Å: Chain A: P.112, M.113, V.114, A.115, F.119, R.143, F.155, M.157, N.159, F.160, F.161, Y.197, W.230 Ligands: ANP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:M.113, A:A.115, A:N.159 Hydrogen bonds: A:P.112, A:V.114, A:N.159, A:N.159 Salt bridges: A:R.143

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pyrrolysine--tRNA ligase