Research workbench
Crystal structure of ragulator complex (P18 76-145)
Analyse Crystal structure of ragulator complex (P18 76-145) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y39
- Type
- protein
- Length
- 903 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
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 10 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ragulator complex protein LAMTOR1 | protein | 67 | 60% helix, 0% strand | Q6IAA8 |
| B | Ragulator complex protein LAMTOR2 | protein | 116 | 39% helix, 31% strand | Q9Y2Q5 |
| C | Ragulator complex protein LAMTOR3 | protein | 121 | 39% helix, 31% strand | Q9UHA4 |
| D | Ragulator complex protein LAMTOR4 | protein | 99 | 25% helix, 36% strand | Q0VGL1 |
| E | Ragulator complex protein LAMTOR5 | protein | 90 | 30% helix, 38% strand | O43504 |
| F | Ragulator complex protein LAMTOR1 | protein | 32 | 66% helix, 0% strand | Q6IAA8 |
| G | Ragulator complex protein LAMTOR2 | protein | 117 | 41% helix, 32% strand | Q9Y2Q5 |
| H | Ragulator complex protein LAMTOR3 | protein | 117 | 36% helix, 32% strand | Q9UHA4 |
| I | Ragulator complex protein LAMTOR4 | protein | 60 | 28% helix, 20% strand | Q0VGL1 |
| J | Ragulator complex protein LAMTOR5 | protein | 84 | 29% helix, 30% strand | O43504 |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.69 | 0.75 | 76 | empty |
| 2 | 720 | 0.69 | 0.76 | 58 | empty |
| 3 | 426 | 0.67 | 0.80 | 36 | empty |
| 4 | 158 | 0.60 | 0.83 | 26 | empty |
| 5 | 94 | 0.59 | 0.87 | 26 | empty |
Interfaces
23 interfaces between chains.
- G–H · 1410 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1344 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1059 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1001 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 896 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5Y39 · Crystal structure of Ragulator complex (p18 76-145) · the same entry in another collection · chain J against J, TM-score 1.00
- Q9UHA4 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR3 (Q9UHA4) · a predicted model of the same protein · chain H against A, TM-score 0.99
- Q9Y2Q5 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR2 (Q9Y2Q5) · a predicted model of the same protein · chain G against A, TM-score 0.98
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 5Y39 · PDBe 5Y39 · UniProt Q6IAA8 · UniProt Q9Y2Q5 · UniProt Q9UHA4 · UniProt Q0VGL1 · UniProt O43504
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