MolNFT v1 · #26953 · protein
Crystal structure of asparaginyl-tRNA synthetase from pyrococcus horikoshii complexed with asparaginyl-adenylate
1X54: “Crystal structure of asparaginyl-tRNA synthetase from pyrococcus horikoshii complexed with…”. X-ray diffraction, 2 ligands (4AD, MG), 4 pockets (best druggability 0.71). MolNFT v1 #26953 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1X54
- 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
- 4AD, MG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Asparaginyl-tRNA synthetase (EC 6.1.1.22) | protein | 434 | 35% helix, 28% strand | O57980 |
Ligands and binding sites
- 4AD · 4-amino-1,4-dioxobutan-2-aminium adenosine-5'-monophosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.71 | 0.81 | 50 | MG, 4AD |
| 2 | 188 | 0.58 | 0.81 | 32 | empty |
| 3 | 55 | 0.49 | 0.86 | 19 | empty |
| 4 | 119 | 0.41 | 0.76 | 17 | empty |
Compared structures
- 1X54 · 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 1X54 · PDBe 1X54 · UniProt O57980
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