MolNFT v1 · #183549 · protein
Crystal structure of neisseria gonorrhoeae leurs E169G mutant in complex with ATP and L-leucinol
7NU3 · Leucine--tRNA ligase: “Crystal structure of neisseria gonorrhoeae leurs E169G mutant in complex with ATP and L-leucinol”. X-ray diffraction, 4 ligands (ATP, DCL, ZN), 7 pockets (best druggability 0.76). MolNFT v1 #183549 on…
- PDB
- 7NU3
- Type
- protein
- Length
- 848 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, ZN, MG
- Pockets
- 7 · best druggability 0.76
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 | 848 | 41% helix, 19% strand | B4RNT1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A
- DCL · 2-amino-4-methyl-pentan-1-ol · 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.76 | 0.78 | 121 | DCL, ATP |
| 2 | 397 | 0.62 | 0.77 | 34 | ATP |
| 3 | 76 | 0.55 | 0.87 | 19 | empty |
| 4 | 118 | 0.40 | 0.75 | 19 | empty |
| 5 | 110 | 0.35 | 0.73 | 20 | empty |
Compared structures
- 7NU3 · Crystal Structure of Neisseria gonorrhoeae LeuRS E169G 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 0.94
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 7NU3 · PDBe 7NU3 · UniProt B4RNT1
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