SMTL ID : 4dpg.3 (3 other biounits)

Crystal Structure of Human LysRS: P38/AIMP2 Complex I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

hetero-2-1-mer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 11 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 10 PLIP interactions: 8 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.431 Hydrogen bonds: A:E.233, A:E.233, A:Y.273, A:N.429, A:E.433, K.1, K.1 Water bridges: A:V.211, A:E.426 LYS.4: 12 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 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.431 Hydrogen bonds: B:G.209, B:G.209, B:N.429, B:E.433, K.4 Water bridges: B:E.271

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.2: 9 residues within 4Å: Chain A: R.255, T.262, H.263, N.264, F.267, E.426, G.482, R.485, I.496 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.255, A:R.255, A:E.257, A:H.263, A:N.264, A:E.426, A:R.485, A:R.485 Water bridges: A:E.426, A:R.485 pi-Stacking: A:F.267, A:F.267 APC.5: 12 residues within 4Å: Chain B: R.255, T.262, H.263, N.264, F.267, D.377, E.385, E.426, G.482, R.485, I.496 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.255, B:N.264, B:N.264, B:E.426, B:E.426, B:R.485, B:R.485 Water bridges: B:R.485 pi-Stacking: B:F.267, B:F.267

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.419, E.426 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.419, A:E.426 MG.6: 3 residues within 4Å: Chain B: E.419, E.426 Ligands: APC.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.419, B:E.426 MG.7: 2 residues within 4Å: Chain B: H.147, H.149 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.147, B:H.149 MG.8: 3 residues within 4Å: Chain A: H.32 Chain C: P.2, M.3 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:P.2, A:H.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ofir-Birin, Y. et al., Structural Switch of Lysyl-tRNA Synthetase between Translation and Transcription. Mol.Cell (2013)

Release Date

2013-02-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
L

Lysine--tRNA ligase

Aminoacyl tRNA synthase complex-interacting multifunctional protein 2

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