MolNFT v1 · #183557 · protein
Crystal structure of neisseria gonorrhoeae leurs L550G mutant in complex with the reaction intermediate leu-AMP
7NUB · Leucine--tRNA ligase: “Crystal structure of neisseria gonorrhoeae leurs L550G mutant in complex with the reaction intermediate…”. X-ray diffraction, 3 ligands (USB, ZN, MG), 6 pockets (best druggability 0.75). MolNFT v1 #183557 on…
- PDB
- 7NUB
- Type
- protein
- Length
- 773 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
- USB, ZN, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 773 | 41% helix, 17% strand | B4RNT1 |
Ligands and binding sites
- USB · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S})-2-azanyl-4-methyl-pentanoate · 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
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 | 429 | 0.75 | 0.84 | 46 | USB |
| 2 | 51 | 0.59 | 0.92 | 18 | empty |
| 3 | 51 | 0.45 | 0.85 | 14 | empty |
| 4 | 99 | 0.39 | 0.76 | 14 | empty |
| 5 | 55 | 0.38 | 0.81 | 17 | empty |
Compared structures
- 7NUB · Crystal Structure of Neisseria gonorrhoeae LeuRS L550G mutant in Complex with the… · 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 0.91
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 7NUB · PDBe 7NUB · UniProt B4RNT1
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