MolNFT v1 · #117887 · protein
Crystal structure of lysyl-tRNA synthetase from cryptosporidium parvum complexed with L-lysine and cladosporin
5ELO · Lysine--tRNA ligase: “Crystal structure of lysyl-tRNA synthetase from cryptosporidium parvum complexed with L-lysine and cladosporin”. X-ray diffraction, 3 ligands (LYS, KRS, SO4), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5ELO
- Type
- protein
- Length
- 1,995 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
- Q5CR27
- Ligands
- LYS, KRS, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 502 | 35% helix, 25% strand | Q5CR27 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 500 | 35% helix, 26% strand | Q5CR27 |
| C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 496 | 35% helix, 26% strand | Q5CR27 |
| D | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 497 | 35% helix, 26% strand | Q5CR27 |
Ligands and binding sites
- LYS · Lysine · ligand · 4 copies · chains A, B, C, D
- KRS · cladosporin · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.84 | 0.87 | 103 | empty |
| 2 | 282 | 0.79 | 0.91 | 60 | empty |
| 3 | 714 | 0.79 | 0.84 | 79 | LYS, KRS |
| 4 | 722 | 0.79 | 0.83 | 81 | LYS, KRS, SO4 |
| 5 | 702 | 0.79 | 0.83 | 78 | LYS, KRS, SO4 |
Interfaces
4 interfaces between chains.
- A–B · 4481 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 4424 Ų buried · 62 hydrogen bonds · protein-protein
- B–D · 277 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 122 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ELO · Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with… · the same entry in another collection · chain A against A, 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 Q5CR27
- Elsewhere: RCSB PDB 5ELO · PDBe 5ELO · UniProt Q5CR27
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