MolNFT v1 · #16863 · protein
Leucyl-tRNA synthetase from thermus thermophilus complexed with a pre-transfer editing substrate analogue in both synthetic active site and editing site
1OBH: “Leucyl-tRNA synthetase from thermus thermophilus complexed with a pre-transfer editing substrate analogue in…”. X-ray diffraction, 4 ligands (NVA, LMS, HG), 3 pockets (best druggability 0.64). MolNFT v1 #16863 on GenesisL1: 3D…
- PDB
- 1OBH
- Type
- protein
- Length
- 762 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-tRNA synthetase
- Ligands
- NVA, LMS, HG, SO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucyl-tRNA synthetase | protein | 762 | 43% helix, 17% strand | — |
Ligands and binding sites
- NVA · Norvaline · ligand · 2 copies · chains A
- LMS · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydro-2-furanyl]methyl sulfamate · ligand · 2 copies · chains A
- HG · Mercury (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.64 | 0.78 | 48 | SO4, NVA, LMS |
| 2 | 253 | 0.55 | 0.77 | 24 | NVA, LMS |
| 3 | 72 | 0.35 | 0.76 | 15 | HG |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1OBH · Leucyl-tRNA synthetase from thermus thermophilus complexed with a pre-transfer editing… · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 1OBH · PDBe 1OBH
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