Research workbench
Crystal structure of ragulator
Analyse Crystal structure of ragulator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B9X
- Type
- protein
- Length
- 488 residues
- Chains
- 5
- 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, A0A0C4DGV4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ragulator complex protein LAMTOR1 | protein | 60 | 52% helix, 2% strand | Q6IAA8 |
| B | Ragulator complex protein LAMTOR2 | protein | 126 | 40% helix, 28% strand | Q9Y2Q5 |
| C | Ragulator complex protein LAMTOR3 | protein | 121 | 40% helix, 30% strand | Q9UHA4 |
| D | Ragulator complex protein LAMTOR4 | protein | 90 | 26% helix, 40% strand | Q0VGL1 |
| E | Hepatitis B virus X interacting protein | protein | 91 | 31% helix, 37% strand | A0A0C4DGV4 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.67 | 0.78 | 46 | empty |
| 2 | 161 | 0.56 | 0.81 | 24 | empty |
| 3 | 125 | 0.48 | 0.79 | 25 | empty |
| 4 | 104 | 0.35 | 0.74 | 16 | empty |
| 5 | 51 | 0.33 | 0.78 | 15 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1333 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 1049 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 980 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 971 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 672 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6B9X · Crystal structure of Ragulator · the same entry in another collection · chain E against E, TM-score 1.00
- Q9UHA4 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR3 (Q9UHA4) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q9Y2Q5 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR2 (Q9Y2Q5) · a predicted model of the same protein · chain B against A, TM-score 0.94
- Q0VGL1 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR4 (Q0VGL1) · a predicted model of the same protein · chain D against A, TM-score 0.94
- Q6IAA8 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR1 (Q6IAA8) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 A0A0C4DGV4
- Elsewhere: RCSB PDB 6B9X · PDBe 6B9X · UniProt Q6IAA8 · UniProt Q9Y2Q5 · UniProt Q9UHA4 · UniProt Q0VGL1 · UniProt A0A0C4DGV4
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