MolNFT v1 · #112865 · protein
The N-terminal extension domain of human asparaginyl-tRNA synthetase
4ZYA · Asparagine--tRNA ligase, cytoplasmic: “The N-terminal extension domain of human asparaginyl-tRNA synthetase”. X-ray diffraction, 2 ligands (ZN, CL), 1 pocket (best druggability 0.65). MolNFT v1 #112865 on GenesisL1: 3D structure…
- PDB
- 4ZYA
- Type
- protein
- Length
- 145 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Asparagine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.22
- UniProt
- O43776
- Ligands
- ZN, CL
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Asparagine--tRNA ligase, cytoplasmic (EC 6.1.1.22) | protein | 69 | 29% helix, 19% strand | O43776 |
| B | Asparagine--tRNA ligase, cytoplasmic (EC 6.1.1.22) | protein | 76 | 28% helix, 17% strand | O43776 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · chains B
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 | 73 | 0.65 | 0.92 | 27 | CL |
Interfaces
1 interface between chains.
- A–B · 832 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4ZYA · The N-terminal extension domain of human asparaginyl-tRNA synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- O43776 · AlphaFold monomer V2.0 prediction for asparagine--tRNA ligase, cytoplasmic (O43776) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 O43776
- Elsewhere: RCSB PDB 4ZYA · PDBe 4ZYA · UniProt O43776
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.