MolNFT v1 · #120957 · protein
Loa loa lysyl-tRNA synthetase in complex with cladosporin.
5HGQ · Lysine--tRNA ligase: “Loa loa lysyl-tRNA synthetase in complex with cladosporin.”. X-ray diffraction, 2 ligands (LYS, KRS), 20 pockets (best druggability 0.80). MolNFT v1 #120957 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5HGQ
- Type
- protein
- Length
- 1,890 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- E1FQP0
- Ligands
- LYS, KRS
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 465 | 28% helix, 26% strand | E1FQP0 |
| D | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 470 | 30% helix, 26% strand | E1FQP0 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 482 | 30% helix, 26% strand | E1FQP0 |
| C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 473 | 28% helix, 27% strand | E1FQP0 |
Ligands and binding sites
- LYS · Lysine · ligand · 4 copies · chains A, D, B, C
- KRS · cladosporin · ligand · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.80 | 0.84 | 114 | empty |
| 2 | 306 | 0.79 | 0.90 | 65 | empty |
| 3 | 830 | 0.78 | 0.82 | 83 | LYS, KRS |
| 4 | 1154 | 0.77 | 0.79 | 110 | LYS, KRS |
| 5 | 699 | 0.74 | 0.80 | 70 | GOL, LYS, KRS |
Interfaces
3 interfaces between chains.
- A–B · 4068 Ų buried · 47 hydrogen bonds · protein-protein
- D–C · 4024 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 1220 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5HGQ · Loa loa Lysyl-tRNA synthetase in complex with Cladosporin. · the same entry in another collection · chain C against C, TM-score 1.00
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 E1FQP0
- Elsewhere: RCSB PDB 5HGQ · PDBe 5HGQ · UniProt E1FQP0
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