MolNFT v1 · #26954 · protein
Crystal structure of asparaginyl-tRNA synthetase from pyrococcus horikoshii complexed with asparaginyl-adenylate analogue
1X55: “Crystal structure of asparaginyl-tRNA synthetase from pyrococcus horikoshii complexed with…”. X-ray diffraction, 3 ligands (NSS, MG, PO4), 6 pockets (best druggability 0.71). MolNFT v1 #26954 on GenesisL1: 3D structure, binding…
- PDB
- 1X55
- Type
- protein
- Length
- 434 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Asparaginyl-tRNA synthetase
- EC
- 6.1.1.22
- UniProt
- O57980
- Ligands
- NSS, MG, PO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Asparaginyl-tRNA synthetase (EC 6.1.1.22) | protein | 434 | 36% helix, 27% strand | O57980 |
Ligands and binding sites
- NSS · 5'-O-[N-(L-asparaginyl)sulfamoyl]adenosine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.71 | 0.81 | 53 | PO4, MG, NSS |
| 2 | 197 | 0.58 | 0.80 | 31 | empty |
| 3 | 77 | 0.45 | 0.81 | 20 | empty |
| 4 | 56 | 0.44 | 0.83 | 23 | empty |
| 5 | 111 | 0.40 | 0.76 | 19 | empty |
Compared structures
- 1X55 · Crystal structure of asparaginyl-tRNA synthetase from Pyrococcus horikoshii complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- O57980 · AlphaFold monomer V2.0 prediction for asparagine--tRNA ligase (O57980) · a predicted model of the same protein · chain A 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 O57980
- Elsewhere: RCSB PDB 1X55 · PDBe 1X55 · UniProt O57980
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