Research workbench
Crystal structure of a truncated form of threonyl-tRNA synthetase with a threonyl adenylate analog
Analyse Crystal structure of a truncated form of threonyl-tRNA synthetase with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EVL
- Type
- protein
- Length
- 1,604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonyl-tRNA synthetase
- EC
- 6.1.1.3
- UniProt
- P0A8M3
- Ligands
- TSB, ZN
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Threonyl-tRNA synthetase (EC 6.1.1.3) | protein | 401 | 38% helix, 27% strand | P0A8M3 |
Ligands and binding sites
- TSB · 5'-O-(N-(L-threonyl)-sulfamoyl)adenosine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.82 | 0.86 | 79 | empty |
| 2 | 903 | 0.81 | 0.83 | 91 | empty |
| 3 | 1146 | 0.78 | 0.80 | 84 | empty |
| 4 | 381 | 0.68 | 0.81 | 47 | empty |
| 5 | 353 | 0.68 | 0.81 | 38 | ZN, TSB |
Interfaces
5 interfaces between chains.
- A–B · 2160 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2151 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 253 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 237 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 153 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1EVL · Crystal structure of a truncated form of threonyl-tRNA synthetase with a threonyl… · the same entry in another collection · chain D against D, TM-score 1.00
- P0A8M3 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase (P0A8M3) · a predicted model of the same protein · chain D 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 P0A8M3
- Elsewhere: RCSB PDB 1EVL · PDBe 1EVL · UniProt P0A8M3
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