Research workbench
Crystal structure of the RNA binding domain of threonyl-tRNA synthetase from cryptosporidium parvum iowa II
Analyse Crystal structure of the RNA binding domain of threonyl-tRNA synthetase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L3O
- Type
- protein
- Length
- 1,602 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
- Q5CYN0
- Ligands
- ZN, CA
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonyl-tRNA synthetase (EC 6.1.1.3) | protein | 400 | 38% helix, 26% strand | Q5CYN0 |
| B, C | Threonyl-tRNA synthetase (EC 6.1.1.3) | protein | 401 | 38% helix, 26% strand | Q5CYN0 |
| D | Threonyl-tRNA synthetase (EC 6.1.1.3) | protein | 400 | 38% helix, 25% strand | Q5CYN0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.83 | 0.85 | 103 | CA |
| 2 | 214 | 0.79 | 0.94 | 34 | CA |
| 3 | 373 | 0.71 | 0.83 | 44 | empty |
| 4 | 343 | 0.69 | 0.83 | 44 | empty |
| 5 | 376 | 0.65 | 0.79 | 40 | ZN |
Interfaces
3 interfaces between chains.
- A–D · 2383 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2371 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 872 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7L3O · Crystal Structure of the RNA binding domain of Threonyl-tRNA synthetase from… · 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 Q5CYN0
- Elsewhere: RCSB PDB 7L3O · PDBe 7L3O · UniProt Q5CYN0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.