Research workbench
Crystal structure of lysyl-tRNA synthetase from cryptosporidium parvum complexed with L-lysine and adenosine
Analyse Crystal structure of lysyl-tRNA synthetase from cryptosporidium parvum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BNI
- Type
- protein
- Length
- 1,001 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, ADN, NA, SO4
- Pockets
- 12 · best druggability 0.81
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 | 502 | 35% helix, 26% strand | Q5CR27 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 499 | 35% helix, 26% strand | Q5CR27 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- ADN · Adenosine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.81 | 0.92 | 62 | EDO |
| 2 | 706 | 0.79 | 0.84 | 76 | LYS, ADN |
| 3 | 656 | 0.78 | 0.83 | 75 | LYS, ADN, EDO |
| 4 | 277 | 0.73 | 0.87 | 37 | EDO |
| 5 | 308 | 0.70 | 0.84 | 39 | EDO |
Interfaces
1 interface between chains.
- A–B · 4382 Ų buried · 60 hydrogen bonds · protein-protein
Compared structures
- 6BNI · Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with… · the same entry in another collection · chain B against B, 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 6BNI · PDBe 6BNI · UniProt Q5CR27
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.