Research workbench
Crystal structure of ragulator complex (P18 49-161)
Analyse Crystal structure of ragulator complex (P18 49-161) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y3A
- Type
- protein
- Length
- 974 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ragulator complex protein LAMTOR1; Ragulator complex protein LAMTOR2; Ragulator complex…
- UniProt
- Q6IAA8, Q9Y2Q5, Q9UHA4, Q0VGL1, O43504
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 8 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ragulator complex protein LAMTOR1 | protein | 74 | 61% helix, 1% strand | Q6IAA8 |
| B | Ragulator complex protein LAMTOR2 | protein | 113 | 39% helix, 30% strand | Q9Y2Q5 |
| C, H | Ragulator complex protein LAMTOR3 | protein | 120 | 38% helix, 31% strand | Q9UHA4 |
| D | Ragulator complex protein LAMTOR4 | protein | 94 | 24% helix, 37% strand | Q0VGL1 |
| E, J | Ragulator complex protein LAMTOR5 | protein | 90 | 29% helix, 36% strand | O43504 |
| F | Ragulator complex protein LAMTOR1 | protein | 70 | 53% helix, 0% strand | Q6IAA8 |
| G | Ragulator complex protein LAMTOR2 | protein | 110 | 40% helix, 33% strand | Q9Y2Q5 |
| I | Ragulator complex protein LAMTOR4 | protein | 93 | 22% helix, 37% strand | Q0VGL1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, D, E, F, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.71 | 0.77 | 76 | empty |
| 2 | 550 | 0.67 | 0.77 | 52 | empty |
| 3 | 201 | 0.56 | 0.79 | 27 | empty |
| 4 | 149 | 0.49 | 0.78 | 26 | empty |
| 5 | 221 | 0.46 | 0.73 | 29 | empty |
Interfaces
22 interfaces between chains.
- B–C · 1451 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1259 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 1089 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1044 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 982 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 Q6IAA8
- Every structure of UniProt Q9Y2Q5
- Every structure of UniProt Q9UHA4
- Every structure of UniProt Q0VGL1
- Every structure of UniProt O43504
- Elsewhere: RCSB PDB 5Y3A · PDBe 5Y3A · UniProt Q6IAA8 · UniProt Q9Y2Q5 · UniProt Q9UHA4 · UniProt Q0VGL1 · UniProt O43504
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.