Research workbench
Crystal structure of hte cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain complex with a post- transfer editing analogue of norvaline (NV2AA)
Analyse Crystal structure of hte cryptosporidium muris cytosolic leucyl-tRNA synthetase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FOG
- Type
- protein
- Length
- 1,118 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-tRNA synthetase
- EC
- 6.1.1.4
- UniProt
- B6AA20
- Ligands
- VRT, K
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 279 | 33% helix, 25% strand | B6AA20 |
| B | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 281 | 32% helix, 27% strand | B6AA20 |
| C | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 274 | 34% helix, 25% strand | B6AA20 |
| D | Leucyl-tRNA synthetase (EC 6.1.1.4) | protein | 284 | 30% helix, 25% strand | B6AA20 |
Ligands and binding sites
- VRT · 2'-(L-norvalyl)amino-2'-deoxyadenosine · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 2 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.83 | 0.84 | 91 | VRT |
| 2 | 449 | 0.74 | 0.84 | 38 | VRT |
| 3 | 332 | 0.74 | 0.86 | 33 | VRT |
| 4 | 355 | 0.72 | 0.84 | 34 | VRT |
| 5 | 565 | 0.67 | 0.77 | 54 | empty |
Interfaces
3 interfaces between chains.
- A–B · 543 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 535 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 259 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5FOG · Crystal structure of hte Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing… · 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 B6AA20
- Elsewhere: RCSB PDB 5FOG · PDBe 5FOG · UniProt B6AA20
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