Research workbench
Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11d
Analyse Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11d in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YKS
- Type
- protein
- Length
- 813 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.97
- Source
- Neisseria gonorrhoeae
- Molecule
- Leucine--tRNA ligase
- EC
- 6.1.1.4
- UniProt
- A0A5K1KQ39
- Ligands
- OVT, ZN, MG
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.97 · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 813 | 42% helix, 19% strand | A0A5K1KQ39 |
Ligands and binding sites
- OVT · [(2~{R},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[3-[4-(2-phenylethyl)-1,2,3-triazol-1-yl]propyl]oxan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.76 | 0.78 | 88 | EDO |
| 2 | 437 | 0.67 | 0.79 | 33 | empty |
| 3 | 309 | 0.64 | 0.80 | 37 | OVT |
| 4 | 69 | 0.44 | 0.82 | 16 | empty |
| 5 | 112 | 0.41 | 0.76 | 23 | empty |
Compared structures
- 6YKS · Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with compound 11D · 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 A0A5K1KQ39
- Elsewhere: RCSB PDB 6YKS · PDBe 6YKS · UniProt A0A5K1KQ39
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.