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Crystal structure of lysyl-tRNA synthetase from cryptosporidium parvum complexed with L-lysylsulfamoyl 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
- 6C86
- Type
- protein
- Length
- 998 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
- KAA, NA, SO4, CL
- Pockets
- 12 · best druggability 0.82
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 | 497 | 35% helix, 26% strand | Q5CR27 |
Ligands and binding sites
- KAA · 5'-O-[(L-lysylamino)sulfonyl]adenosine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.82 | 0.89 | 87 | EDO |
| 2 | 693 | 0.79 | 0.84 | 80 | KAA |
| 3 | 633 | 0.78 | 0.84 | 75 | KAA |
| 4 | 277 | 0.68 | 0.83 | 32 | empty |
| 5 | 122 | 0.63 | 0.87 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 4315 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 6C86 · 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 6C86 · PDBe 6C86 · UniProt Q5CR27
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