MolNFT v1 · #104179 · protein
Crystal structure of arginyl-tRNA synthetase complexed with L-arginine
4Q2T · Arginine--tRNA ligase, cytoplasmic: “Crystal structure of arginyl-tRNA synthetase complexed with L-arginine”. X-ray diffraction, 1 ligand (ARG), 19 pockets (best druggability 0.77). MolNFT v1 #104179 on GenesisL1: 3D structure…
- PDB
- 4Q2T
- Type
- protein
- Length
- 1,178 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.19
- UniProt
- P54136
- Ligands
- ARG
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine--tRNA ligase, cytoplasmic (EC 6.1.1.19) | protein | 590 | 52% helix, 12% strand | P54136 |
| B | Arginine--tRNA ligase, cytoplasmic (EC 6.1.1.19) | protein | 588 | 53% helix, 11% strand | P54136 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.77 | 0.83 | 45 | empty |
| 2 | 583 | 0.64 | 0.75 | 48 | empty |
| 3 | 290 | 0.61 | 0.79 | 53 | ARG, GOL |
| 4 | 314 | 0.60 | 0.78 | 47 | empty |
| 5 | 178 | 0.59 | 0.82 | 40 | ARG, GOL |
Interfaces
1 interface between chains.
- A–B · 1389 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4Q2T · Crystal structure of Arginyl-tRNA synthetase complexed with L-arginine · the same entry in another collection · chain A against A, TM-score 1.00
- P54136 · AlphaFold monomer V2.0 prediction for arginine--tRNA ligase, cytoplasmic (P54136) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P54136
- Elsewhere: RCSB PDB 4Q2T · PDBe 4Q2T · UniProt P54136
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.