MolNFT v1 · #182692 · protein
Crystal structure of the M. abscessus leurs editing domain in complex with epetraborole-AMP adduct
7N12 · Leucine--tRNA ligase: “Crystal structure of the M. abscessus leurs editing domain in complex with epetraborole-AMP adduct”. X-ray diffraction, 2 ligands (365, SO4), 5 pockets (best druggability 0.55). MolNFT v1 #182692 on GenesisL1…
- PDB
- 7N12
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine--tRNA ligase
- EC
- 6.1.1.4
- UniProt
- A0A0U0XQP3
- Ligands
- 365, SO4
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 188 | 29% helix, 23% strand | A0A0U0XQP3 |
Ligands and binding sites
- 365 · [(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-6-(6-aminopurin-9-yl)-2'-(3-oxidanylpropoxy)spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-yl]methyl dihydrogen phosphate · ligand · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.55 | 0.80 | 20 | 365 |
| 2 | 159 | 0.52 | 0.79 | 20 | 365 |
| 3 | 115 | 0.37 | 0.74 | 21 | empty |
| 4 | 69 | 0.32 | 0.74 | 19 | empty |
| 5 | 51 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 93 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7N12 · Crystal structure of the M. abscessus LeuRS editing domain in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A0U0XQP3
- Elsewhere: RCSB PDB 7N12 · PDBe 7N12 · UniProt A0A0U0XQP3
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