Research workbench
Crystal structure of human lysrs: P38/AIMP2 complex II
Analyse Crystal structure of human lysrs: P38/AIMP2 complex II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ILD
- Type
- protein
- Length
- 1,030 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase; Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
- EC
- 2.7.7.-, 6.1.1.6
- UniProt
- Q15046, Q13155
- Ligands
- LYS, 45A, MG
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 2.7.7.-, 6.1.1.6) | protein | 501 | 36% helix, 26% strand | Q15046 |
| B | Lysine--tRNA ligase (EC 2.7.7.-, 6.1.1.6) | protein | 499 | 36% helix, 26% strand | Q15046 |
| C | Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | protein | 30 | 0% helix, 0% strand | Q13155 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- 45A · 5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.85 | 0.91 | 85 | empty |
| 2 | 851 | 0.79 | 0.82 | 80 | LYS, GOL, MG |
| 3 | 831 | 0.78 | 0.82 | 77 | LYS, MG, GOL, 45A |
| 4 | 282 | 0.73 | 0.86 | 39 | empty |
| 5 | 90 | 0.71 | 0.94 | 30 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 4372 Ų buried · 77 hydrogen bonds · protein-protein
- A–C · 678 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 398 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6ILD · Crystal Structure of Human LysRS: P38/AIMP2 Complex II · the same entry in another collection · chain A against A, TM-score 1.00
- Q15046 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase (Q15046) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q13155 · AlphaFold monomer V2.0 prediction for aminoacyl tRNA synthase complex-interacting… · a predicted model of the same protein · chain C against A, TM-score 0.26
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q15046
- Every structure of UniProt Q13155
- Elsewhere: RCSB PDB 6ILD · PDBe 6ILD · UniProt Q15046 · UniProt Q13155
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