MolNFT v1 · #16859 · protein
Leucyl-tRNA synthetase from thermus thermophilus complexed with a post-transfer editing substrate analogue
1OBC: “Leucyl-tRNA synthetase from thermus thermophilus complexed with a post-transfer editing substrate analogue”. X-ray diffraction, 5 ligands (LEU, NVA, 2AD), 5 pockets (best druggability 0.72). MolNFT v1 #16859 on GenesisL1: 3D…
- PDB
- 1OBC
- Type
- protein
- Length
- 811 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-tRNA synthetase
- Ligands
- LEU, NVA, 2AD, LMS, ZN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucyl-tRNA synthetase | protein | 811 | 42% helix, 20% strand | — |
Ligands and binding sites
- LEU · Leucine · ligand · chains A
- NVA · Norvaline · ligand · chains A
- 2AD · 2'-amino-2'-deoxyadenosine · ligand · chains A
- LMS · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydro-2-furanyl]methyl sulfamate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
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 | 745 | 0.72 | 0.78 | 64 | LEU, LMS |
| 2 | 278 | 0.61 | 0.79 | 34 | NVA, 2AD |
| 3 | 173 | 0.45 | 0.75 | 21 | empty |
| 4 | 70 | 0.39 | 0.79 | 16 | empty |
| 5 | 97 | 0.34 | 0.73 | 17 | empty |
Compared structures
- 1OBC · Leucyl-tRNA synthetase from thermus thermophilus complexed with a post-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 1OBC · PDBe 1OBC
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