Research workbench
Asparaginyl-tRNA synthetase from brugia malayi complexed with the sulphamoyl analogue of asparaginyl-adenylate
Analyse Asparaginyl-tRNA synthetase from brugia malayi complexed with the sulphamoyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XGT
- Type
- protein
- Length
- 860 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Asparaginyl-tRNA synthetase, cytoplasmic
- EC
- 6.1.1.4
- UniProt
- A8PWE4
- Ligands
- NSS, MG
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Asparaginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.4) | protein | 427 | 36% helix, 28% strand | A8PWE4 |
| B | Asparaginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.4) | protein | 433 | 35% helix, 28% strand | A8PWE4 |
Ligands and binding sites
- NSS · 5'-O-[N-(L-asparaginyl)sulfamoyl]adenosine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.82 | 0.95 | 44 | empty |
| 2 | 830 | 0.75 | 0.79 | 83 | empty |
| 3 | 481 | 0.71 | 0.81 | 50 | NSS, MG |
| 4 | 447 | 0.70 | 0.81 | 51 | NSS, MG |
| 5 | 74 | 0.51 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4016 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 2XGT · Asparaginyl-tRNA synthetase from Brugia malayi complexed with the sulphamoyl analogue of… · the same entry in another collection · chain A against A, TM-score 1.00
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 A8PWE4
- Elsewhere: RCSB PDB 2XGT · PDBe 2XGT · UniProt A8PWE4
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