Research workbench
Crystal structure of the P.FALCIPARUM cytosolic leucyl-tRNA synthetase editing domain (space group P1) containing deletions of insertions 1 and 3
Analyse Crystal structure of the P.FALCIPARUM cytosolic leucyl-tRNA synthetase editing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FOD
- Type
- protein
- Length
- 619 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-tRNA synthetase
- EC
- 6.1.1.4
- UniProt
- C6KT64
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 303 | 39% helix, 22% strand | C6KT64 |
| B | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 316 | 38% helix, 21% strand | C6KT64 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.77 | 0.81 | 60 | empty |
| 2 | 363 | 0.73 | 0.85 | 36 | EDO |
| 3 | 72 | 0.40 | 0.79 | 16 | empty |
| 4 | 79 | 0.40 | 0.78 | 19 | empty |
| 5 | 73 | 0.34 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 637 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5FOD · Crystal structure of the P.falciparum cytosolic leucyl-tRNA synthetase editing domain… · 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 C6KT64
- Elsewhere: RCSB PDB 5FOD · PDBe 5FOD · UniProt C6KT64
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