SMTL ID : 6ild.1

Crystal Structure of Human LysRS: P38/AIMP2 Complex II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-2-1-mer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 13 residues within 4Å: Chain A: G.209, A.210, A.231, E.233, E.271, Y.273, N.429, Y.431, E.433, G.478, W.479, G.480 Ligands: GOL.5 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.431 Hydrogen bonds: A:G.209, A:G.209, A:E.233, A:E.271, A:Y.273, A:N.429, A:E.433, K.1 Water bridges: A:Y.431 LYS.6: 14 residues within 4Å: Chain B: G.209, A.210, A.231, E.233, E.271, Y.273, N.429, Y.431, E.433, G.478, W.479, G.480 Ligands: GOL.8, 45A.10 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:Y.431 Hydrogen bonds: B:G.209, B:N.429, B:E.433

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: R.63, H.65, R.80, G.81, E.82, G.83, L.166, I.167, R.173 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.63, A:G.81, A:G.83, A:V.84, A:L.166, A:R.173 Water bridges: A:D.170 GOL.3: 6 residues within 4Å: Chain A: R.255, T.262, H.263, N.264, F.267, I.496 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.255, A:N.264, A:N.264 GOL.5: 9 residues within 4Å: Chain A: T.269, E.426, I.427, C.428, N.429, G.480, M.481, G.482 Ligands: LYS.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.426, A:E.426, A:I.427 Water bridges: A:T.269, A:E.271, A:G.482 GOL.8: 10 residues within 4Å: Chain B: T.269, E.426, I.427, C.428, N.429, G.480, M.481, G.482 Ligands: LYS.6, 45A.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.271, B:E.271, B:C.428 Water bridges: B:I.427, B:G.482 GOL.9: 6 residues within 4Å: Chain B: Y.279, M.283, R.325, N.327, C.395, D.396 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.325, B:N.327, B:D.396 Water bridges: B:Y.279, B:H.280, B:R.325

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: E.419, E.426 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.419, A:E.426, H2O.4, H2O.10, H2O.13, H2O.13 MG.7: 4 residues within 4Å: Chain B: R.417, E.419, E.426 Ligands: 45A.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.419, B:E.426, H2O.19, H2O.20, H2O.27

1 x 45A: 5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine(Non-covalent)

45A.10: 13 residues within 4Å: Chain B: A.210, R.255, T.262, H.263, N.264, F.267, T.269, E.426, R.485, I.496 Ligands: LYS.6, MG.7, GOL.8 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:N.264, K.6 Water bridges: B:R.255, B:R.255, B:R.255, B:D.377, B:E.426, B:G.482, B:D.484, B:R.485 pi-Stacking: B:F.267, B:F.267 pi-Cation interactions: B:R.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hei, Z. et al., Retractile lysyl-tRNA synthetase-AIMP2 assembly in the human multi-aminoacyl-tRNA synthetase complex. J. Biol. Chem. (2019)

Release Date

2019-02-27

Peptides

Lysine--tRNA ligase: AB
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Lysine--tRNA ligase

Aminoacyl tRNA synthase complex-interacting multifunctional protein 2

Related Entries With Identical Sequence