MolNFT v2 · #172557 · protein
Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11b
6YKN · Leucine--tRNA ligase: “Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11b”. X-ray diffraction at 2.63, 3 ligands (OV8, MG, ZN), 7 pockets (best druggability 0.77). MolNFT v2 #172557 on GenesisL1: 3D structure…
- PDB
- 6YKN
- Type
- protein
- Length
- 844 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.63
- Source
- Neisseria gonorrhoeae
- Molecule
- Leucine--tRNA ligase
- EC
- 6.1.1.4
- UniProt
- A0A5K1KQ39
- Ligands
- OV8, MG, ZN
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.63 · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 844 | 41% helix, 20% strand | A0A5K1KQ39 |
Ligands and binding sites
- OV8 · [(2~{R},3~{S},4~{S},5~{R})-5-[3-[4-(aminomethyl)-1,2,3-triazol-1-yl]propyl]-3,4-bis(oxidanyl)oxan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- ZN · Zinc 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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.77 | 0.81 | 88 | EDO |
| 2 | 280 | 0.66 | 0.82 | 38 | OV8 |
| 3 | 56 | 0.48 | 0.86 | 15 | empty |
| 4 | 82 | 0.43 | 0.80 | 21 | empty |
| 5 | 106 | 0.40 | 0.76 | 23 | empty |
Compared structures
- 6YKN · Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with compound 11B · 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 6YKN · PDBe 6YKN · UniProt A0A5K1KQ39
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