MolNFT v1 · #106172 · protein
N-terminal editing domain of threonyl-tRNA synthetase from aeropyrum pernix with L-THR3AA (snapshot 1)
4RRA · Probable threonine--tRNA ligase 2: “N-terminal editing domain of threonyl-tRNA synthetase from aeropyrum pernix with L-THR3AA (snapshot 1)”. X-ray diffraction, 2 ligands (A3T, MG), 1 pocket (best druggability 0.52). MolNFT v1…
- PDB
- 4RRA
- Type
- protein
- Length
- 136 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable threonine--tRNA ligase 2
- EC
- 6.1.1.3
- UniProt
- Q9YFY3
- Ligands
- A3T, MG
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable threonine--tRNA ligase 2 (EC 6.1.1.3) | protein | 136 | 25% helix, 40% strand | Q9YFY3 |
Ligands and binding sites
- A3T · 3'-deoxy-3'-(L-threonylamino)adenosine · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.52 | 0.79 | 23 | A3T |
Compared structures
- 4RRA · N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YFY3 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase editing subunit (Q9YFY3) · 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 Q9YFY3
- Elsewhere: RCSB PDB 4RRA · PDBe 4RRA · UniProt Q9YFY3
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