MolNFT v1 · #170846 · protein
Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with compound 11C
6YKQ · Leucine--tRNA ligase: “Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with compound 11C”. X-ray diffraction, 3 ligands (OVW, ZN, MG), 8 pockets (best druggability 0.77). MolNFT v1 #170846 on GenesisL1: 3D structure, binding…
- PDB
- 6YKQ
- Type
- protein
- Length
- 847 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine--tRNA ligase
- EC
- 6.1.1.4
- UniProt
- A0A5K1KQ39
- Ligands
- OVW, ZN, MG
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 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 | 847 | 41% helix, 20% strand | A0A5K1KQ39 |
Ligands and binding sites
- OVW · [(2~{R},3~{S},4~{S},5~{R})-5-[3-(4-octyl-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
- 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 | 1184 | 0.77 | 0.79 | 99 | OVW, EDO |
| 2 | 453 | 0.68 | 0.79 | 35 | empty |
| 3 | 122 | 0.50 | 0.80 | 24 | empty |
| 4 | 59 | 0.48 | 0.85 | 14 | empty |
| 5 | 99 | 0.40 | 0.76 | 22 | empty |
Compared structures
- 6YKQ · Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11c · 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 6YKQ · PDBe 6YKQ · UniProt A0A5K1KQ39
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