Research workbench
Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with 5'-O-(N- (L-leucyl)-SULFAMOYL)CYTIDINE
Analyse Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with 5'-O-(N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q8A
- Type
- protein
- Length
- 820 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
- B4RNT1
- Ligands
- HQ5, ZN, MG
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 820 | 42% helix, 18% strand | B4RNT1 |
Ligands and binding sites
- HQ5 · 5'-O-(N-(L-Leucyl)-Sulfamoyl)Cytidine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.77 | 0.81 | 83 | empty |
| 2 | 227 | 0.65 | 0.83 | 36 | HQ5 |
| 3 | 60 | 0.50 | 0.86 | 18 | empty |
| 4 | 111 | 0.44 | 0.78 | 21 | empty |
| 5 | 117 | 0.37 | 0.73 | 19 | empty |
Compared structures
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 B4RNT1
- Elsewhere: RCSB PDB 6Q8A · PDBe 6Q8A · UniProt B4RNT1
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