MolNFT v1 · #151077 · protein
Crystal structure of lysyl-tRNA synthetase from cryptosporidium parvum complexed with L-lysine and a difluoro cyclohexyl chromone ligand
6HCW · Lysine--tRNA ligase: “Crystal structure of lysyl-tRNA synthetase from cryptosporidium parvum complexed with L-lysine and a difluoro…”. X-ray diffraction, 2 ligands (LYS, FYB), 13 pockets (best druggability 0.80). MolNFT v1 #151077…
- PDB
- 6HCW
- Type
- protein
- Length
- 997 residues
- Chains
- 2
- 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, FYB
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 501 | 35% helix, 26% strand | Q5CR27 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 496 | 35% helix, 26% strand | Q5CR27 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- FYB · ~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.80 | 0.91 | 60 | empty |
| 2 | 684 | 0.79 | 0.84 | 80 | LYS, FYB |
| 3 | 744 | 0.79 | 0.83 | 79 | LYS, FYB |
| 4 | 185 | 0.72 | 0.89 | 27 | empty |
| 5 | 240 | 0.67 | 0.84 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 4447 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 6HCW · 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 6HCW · PDBe 6HCW · UniProt Q5CR27
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