MolNFT v1 · #10902 · protein
Crystal structure of glycyl-tRNA synthetase alpha chain (TM0216) from thermotoga maritima at 1.95 a resolution
1J5W: “Crystal structure of glycyl-tRNA synthetase alpha chain (TM0216) from thermotoga maritima at 1.95 a resolution”. X-ray diffraction, 7 pockets (best druggability 0.76). MolNFT v1 #10902 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1J5W
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycyl-tRNA synthetase alpha chain
- EC
- 6.1.1.14
- UniProt
- Q9WY59
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycyl-tRNA synthetase alpha chain (EC 6.1.1.14) | protein | 276 | 49% helix, 23% strand | Q9WY59 |
| B | Glycyl-tRNA synthetase alpha chain (EC 6.1.1.14) | protein | 278 | 49% helix, 22% strand | Q9WY59 |
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.76 | 0.97 | 25 | empty |
| 2 | 81 | 0.75 | 0.97 | 22 | empty |
| 3 | 76 | 0.75 | 0.98 | 21 | empty |
| 4 | 181 | 0.69 | 0.88 | 27 | empty |
| 5 | 195 | 0.69 | 0.87 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2537 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1J5W · Crystal structure of Glycyl-tRNA synthetase alpha chain (TM0216) from Thermotoga maritima… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WY59 · AlphaFold monomer V2.0 prediction for glycine--tRNA ligase alpha subunit (Q9WY59) · 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 Q9WY59
- Elsewhere: RCSB PDB 1J5W · PDBe 1J5W · UniProt Q9WY59
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