MolNFT v1 · #170840 · protein
Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with compound 15
6YKK · Leucine--tRNA ligase: “Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with compound 15”. X-ray diffraction, 3 ligands (OVK, MG, ZN), 8 pockets (best druggability 0.78). MolNFT v1 #170840 on GenesisL1: 3D structure, binding…
- PDB
- 6YKK
- Type
- protein
- Length
- 826 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
- OVK, MG, ZN
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 826 | 43% helix, 19% strand | A0A5K1KQ39 |
Ligands and binding sites
- OVK · [(2~{R},3~{S},4~{R},5~{S})-3,4-bis(oxidanyl)-5-[2-(5-phenyl-1,2,3,4-tetrazol-2-yl)ethyl]oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate · ligand · chains A
- MG · Magnesium ion · metal
- 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.78 | 0.81 | 105 | OVK, EDO |
| 2 | 304 | 0.68 | 0.83 | 33 | empty |
| 3 | 58 | 0.48 | 0.85 | 15 | empty |
| 4 | 96 | 0.48 | 0.81 | 22 | empty |
| 5 | 111 | 0.39 | 0.75 | 26 | empty |
Compared structures
- 6YKK · Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 15 · 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 6YKK · PDBe 6YKK · UniProt A0A5K1KQ39
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