Research workbench
Crystal structure of neisseria gonorrhoeae leurs L550G mutant in complex with ATP and L-leucinol
Analyse Crystal structure of neisseria gonorrhoeae leurs L550G mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NUC
- Type
- protein
- Length
- 862 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
- ATP, DCL, MG, ZN
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 862 | 38% helix, 20% strand | B4RNT1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- DCL · 2-amino-4-methyl-pentan-1-ol · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.75 | 0.80 | 85 | ATP, MG, DCL |
| 2 | 76 | 0.55 | 0.87 | 19 | empty |
| 3 | 151 | 0.50 | 0.78 | 18 | empty |
| 4 | 100 | 0.34 | 0.73 | 23 | empty |
| 5 | 60 | 0.33 | 0.77 | 17 | empty |
Compared structures
- 7NUC · Crystal Structure of Neisseria gonorrhoeae LeuRS L550G mutant in Complex with ATP and… · the same entry in another collection · chain A against A, TM-score 1.00
- B4RNT1 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase (B4RNT1) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 7NUC · PDBe 7NUC · UniProt B4RNT1
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