MolNFT v1 · #183555 · protein
Crystal structure of neisseria gonorrhoeae leurs in complex with ATP and L-leucinol
7NU9 · Leucine--tRNA ligase: “Crystal structure of neisseria gonorrhoeae leurs in complex with ATP and L-leucinol”. X-ray diffraction, 4 ligands (ATP, DCL, MG), 8 pockets (best druggability 0.76). MolNFT v1 #183555 on GenesisL1: 3D…
- PDB
- 7NU9
- Type
- protein
- Length
- 867 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
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 867 | 40% 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
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 | 759 | 0.76 | 0.80 | 82 | ATP, MG, DCL |
| 2 | 54 | 0.63 | 0.93 | 20 | empty |
| 3 | 222 | 0.50 | 0.75 | 33 | empty |
| 4 | 62 | 0.48 | 0.85 | 16 | empty |
| 5 | 69 | 0.34 | 0.76 | 19 | empty |
Compared structures
- 7NU9 · Crystal Structure of Neisseria gonorrhoeae LeuRS in Complex with ATP and L-leucinol · 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 0.85
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 7NU9 · PDBe 7NU9 · UniProt B4RNT1
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