Research workbench
Crystal structure of the archaeal asparagine synthetase a complexed with L-aspartic acid
Analyse Crystal structure of the archaeal asparagine synthetase a complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P8V
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Asns-like asparaginyl-tRNA synthetase related protein
- UniProt
- Q9V228
- Ligands
- ASP
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Asns-like asparaginyl-tRNA synthetase related protein | protein | 294 | 37% helix, 23% strand | Q9V228 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.82 | 0.94 | 50 | ASP |
| 2 | 236 | 0.81 | 0.94 | 46 | ASP |
| 3 | 50 | 0.72 | 0.99 | 18 | empty |
| 4 | 70 | 0.34 | 0.76 | 17 | empty |
| 5 | 69 | 0.34 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2926 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3P8V · Crystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid · 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 Q9V228
- Elsewhere: RCSB PDB 3P8V · PDBe 3P8V · UniProt Q9V228
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