MolNFT v1 · #113481 · protein
Crystal structure of the leurs editing domain of mycobacterium tuberculosis in complex with the adduct (S)-3-(aminomethyl)-7- ETHOXYBENZO[C][1,2]OXABOROL-1(3H)-ol-AMP
5AGR · Leucine--tRNA ligase: “Crystal structure of the leurs editing domain of mycobacterium tuberculosis in complex with the adduct…”. X-ray diffraction, 1 ligand (A52), 1 pocket (best druggability 0.50). MolNFT v1 #113481 on GenesisL1…
- PDB
- 5AGR
- Type
- protein
- Length
- 192 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
- P9WFV1
- Ligands
- A52
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 192 | 30% helix, 22% strand | P9WFV1 |
Ligands and binding sites
- A52 · 3-AMINOMETHYL-7-(ETHOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine · ligand · 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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.50 | 0.79 | 20 | A52 |
Compared structures
- 5AGR · Crystal structure of the LeuRS editing domain of Mycobacterium tuberculosis in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WFV1 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase (P9WFV1) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P9WFV1
- Elsewhere: RCSB PDB 5AGR · PDBe 5AGR · UniProt P9WFV1
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