Research workbench
Crystal structure of tryptophanyl-tRNA synthetase from thermus thermophilus
Analyse Crystal structure of tryptophanyl-tRNA synthetase from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EL7
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophanyl-tRNA synthetase
- EC
- 6.1.1.2
- UniProt
- Q5SIY7
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 318 | 61% helix, 8% strand | Q5SIY7 |
| B | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 316 | 58% helix, 8% strand | Q5SIY7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 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 | 717 | 0.75 | 0.80 | 65 | empty |
| 2 | 690 | 0.74 | 0.80 | 57 | empty |
| 3 | 122 | 0.41 | 0.76 | 27 | empty |
| 4 | 54 | 0.31 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2152 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2EL7 · Crystal structure of Tryptophanyl-tRNA synthetase from Thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5SIY7
- Elsewhere: RCSB PDB 2EL7 · PDBe 2EL7 · UniProt Q5SIY7
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