MolNFT v1 · #57858 · protein + RNA
Crystal structure of thermotoga maritima nondiscriminating glutamyl- tRNA synthetase in complex with trnagln and a glutamyl-AMP analog
3AKZ · Glutamyl-tRNA synthetase 2: “Crystal structure of thermotoga maritima nondiscriminating glutamyl- tRNA synthetase in complex with trnagln…”. X-ray diffraction, 1 ligand (GSU), 20 pockets (best druggability 0.86). MolNFT v1 #57858 on…
- PDB
- 3AKZ
- Type
- protein + RNA
- Length
- 2,148 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamyl-tRNA synthetase 2; Trnagln
- EC
- 6.1.1.17
- UniProt
- Q9X2I8
- Ligands
- GSU
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, C, A | Glutamyl-tRNA synthetase 2 (EC 6.1.1.17) | protein | 463 | 43% helix, 12% strand | Q9X2I8 |
| F, H, G, E | Trnagln | rna | 74 | — | — |
Ligands and binding sites
- GSU · O5'-(L-glutamyl-sulfamoyl)-adenosine · ligand · 4 copies · chains B, F, D, H, C, G, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.86 | 0.87 | 79 | empty |
| 2 | 615 | 0.82 | 0.88 | 67 | empty |
| 3 | 787 | 0.81 | 0.85 | 67 | GSU |
| 4 | 449 | 0.79 | 0.87 | 42 | GSU |
| 5 | 386 | 0.76 | 0.86 | 39 | GSU |
Interfaces
15 interfaces between chains.
- A–E · 2427 Ų buried · 60 hydrogen bonds · protein-nucleic
- C–G · 2427 Ų buried · 54 hydrogen bonds · protein-nucleic
- D–H · 2405 Ų buried · 43 hydrogen bonds · protein-nucleic
- B–F · 2349 Ų buried · 57 hydrogen bonds · protein-nucleic
- C–A · 794 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3AKZ · Crystal structure of Thermotoga maritima nondiscriminating glutamyl-tRNA synthetase in… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9X2I8 · AlphaFold monomer V2.0 prediction for glutamate--tRNA ligase 2 (Q9X2I8) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q9X2I8
- Elsewhere: RCSB PDB 3AKZ · PDBe 3AKZ · UniProt Q9X2I8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.