MolNFT v1 · #161244 · protein
Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with the intermediate analog 5'-O-(N-(L-leucyl)-SULFAMOYL)ADENOSINE
6Q89 · Leucine--tRNA ligase: “Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with the intermediate analog…”. X-ray diffraction, 3 ligands (LSS, ZN, MG), 6 pockets (best druggability 0.74). MolNFT v1 #161244 on GenesisL1: 3D…
- PDB
- 6Q89
- Type
- protein
- Length
- 852 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
- A0A1D3HNX6
- Ligands
- LSS, ZN, MG
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 852 | 41% helix, 19% strand | A0A1D3HNX6 |
Ligands and binding sites
- LSS · 5'-O-(L-leucylsulfamoyl)adenosine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.74 | 0.77 | 120 | LSS |
| 2 | 399 | 0.60 | 0.76 | 35 | empty |
| 3 | 67 | 0.50 | 0.85 | 15 | empty |
| 4 | 175 | 0.47 | 0.76 | 34 | empty |
| 5 | 62 | 0.31 | 0.75 | 14 | empty |
Compared structures
- 6Q89 · Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with the Intermediate Analog… · 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 A0A1D3HNX6
- Elsewhere: RCSB PDB 6Q89 · PDBe 6Q89 · UniProt A0A1D3HNX6
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