MolNFT v1 · #57289 · protein
Crystal structure of putative threonyl-tRNA synthetase thrrs-1 from aeropyrum pernix (selenomethionine derivative)
3A31 · Probable threonyl-tRNA synthetase 1: “Crystal structure of putative threonyl-tRNA synthetase thrrs-1 from aeropyrum pernix (selenomethionine…”. X-ray diffraction, 2 ligands (ZN, SO4), 5 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 3A31
- Type
- protein
- Length
- 465 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable threonyl-tRNA synthetase 1
- EC
- 6.1.1.3
- UniProt
- Q9YDW0
- Ligands
- ZN, SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable threonyl-tRNA synthetase 1 (EC 6.1.1.3) | protein | 465 | 41% helix, 27% strand | Q9YDW0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.70 | 0.79 | 46 | empty |
| 2 | 123 | 0.61 | 0.85 | 23 | empty |
| 3 | 137 | 0.54 | 0.81 | 27 | empty |
| 4 | 93 | 0.35 | 0.74 | 17 | empty |
| 5 | 53 | 0.25 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 3A31 · Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YDW0 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase catalytic subunit (Q9YDW0) · 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 Q9YDW0
- Elsewhere: RCSB PDB 3A31 · PDBe 3A31 · UniProt Q9YDW0
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