Research workbench
Crystal structure of arginyl-tRNA synthetase from klebsiella pneumoniae subsp. pneumoniae
Analyse Crystal structure of arginyl-tRNA synthetase from klebsiella pneumoniae subsp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GDZ
- Type
- protein
- Length
- 423 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginyl-tRNA synthetase
- EC
- 6.1.1.19
- UniProt
- A6TB43
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginyl-tRNA synthetase (EC 6.1.1.19) | protein | 106 | 45% helix, 18% strand | A6TB43 |
| B | Arginyl-tRNA synthetase (EC 6.1.1.19) | protein | 107 | 48% helix, 18% strand | A6TB43 |
| C | Arginyl-tRNA synthetase (EC 6.1.1.19) | protein | 106 | 48% helix, 18% strand | A6TB43 |
| D | Arginyl-tRNA synthetase (EC 6.1.1.19) | protein | 104 | 46% helix, 18% strand | A6TB43 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.67 | 0.85 | 33 | empty |
| 2 | 113 | 0.42 | 0.77 | 20 | empty |
| 3 | 56 | 0.25 | 0.72 | 11 | empty |
Interfaces
5 interfaces between chains.
- B–C · 717 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 623 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 372 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 133 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3GDZ · Crystal structure of arginyl-tRNA synthetase from Klebsiella pneumoniae subsp. pneumoniae · the same entry in another collection · chain D against D, TM-score 1.00
- A6TB43 · AlphaFold monomer V2.0 prediction for arginine--tRNA ligase (A6TB43) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 A6TB43
- Elsewhere: RCSB PDB 3GDZ · PDBe 3GDZ · UniProt A6TB43
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.